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Conklin, Mike (GfK)

2017-Jun-22 15:15 UTC

[R] Missing dependencies in pkg installs

Following Duncan's instructions I find that the system and R find that
configure IS executable but if trying to install via install.packages I get the
same error.
I also tried using R CMD INSTALL from the terminal and install.packages with a
local file pointing to the very same tar.gz file that shows the executable bit
set. All result in the same "configure is not executable" result.

[meconk at dcex1102shinypr ~]$ ls -l stringi/configure
-rwxr-xr-x 1 meconk meconk 173757 Apr  7 11:43 stringi/configure
[meconk at dcex1102shinypr ~]$ sudo R
[sudo] password for meconk:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]
> getwd()
[1] "/home/meconk"> file_test("-x","stringi/configure")stringi/configure
             TRUE> install.packages("stringi")                                      
Installing package into '/usr/lib64/R/library'(as 'lib' is unspecified)
trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
=================================================downloaded 3.5 MB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: 'configure' exists but is not executable -- see the 'R
Installation and Administration Manual'
* removing '/usr/lib64/R/library/stringi'

The downloaded source packages are in
        '/tmp/Rtmpxw9twb/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
  installation of package 'stringi' had non-zero exit status

--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK 
T +1 763 417 4545 | M +1 612 567 8287 

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Duncan
Murdoch
Sent: Thursday, June 22, 2017 8:23 AM
To: Martin Maechler; David Winsemius
Cc: r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

The "configure exists but is not executable" problem is somewhat
common on Windows, because there's usually no such thing as an executable
bit there.  (Cygwin does something to fake one, but Windows generally
doesn't.)  If you create a tarball there by default you get no executable
bits marked in it.

For a long time, R CMD build has dealt with this issue by using the internal
tar() function.  It corrects the executable bit with a warning during the build.

So if people are getting that error, something has gone wrong.  A few
guesses:

  - They are on Linux but using a mount of a Windows volume that doesn't
preserve the bit.

  - They are using a tarball produced in some strange way on Windows, e.g. by
calling tar directly instead of R CMD build.

  - There's a bug in R in detecting the executable bit.

Martin saw configure marked executable in the tarball from CRAN, which means the
second is unlikely (unless it was very recently fixed), but the first is still
possible.  One test is to manually expand the tarball, then use both ls and
R's test to see if the executable bit is set and is detected by R.  For
example, after downloading stringi_1.1.5.tar.gz you expand it using

tar zxvf stringi_1.1.5.tar.gz

and use

ls -l stringi/configure

to see if the system thinks it is executable, and in R,

file_test("-x", "stringi/configure")

to see what R sees.

Duncan Murdoch

On 22/06/2017 3:38 AM, Martin Maechler wrote:>>>>>> David Winsemius <dwinsemius at comcast.net>
>>>>>>     on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>
>     >> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)
<Mike.Conklin at gfk.com> wrote:
>     >>
>     >> I have a Ubuntu server with an R installation that has 384
packages installed.  We are trying to replicate the system on a Red Hat
Enterprise server. I downloaded the list of packages from the Ubuntu machine and
read it into an R session on the new machine. Then I ran
install.packages(listofpackages).  Now I have 352 packages on the new machine
but several very common packages (like much of the tidyverse, ggplot2, Hmisc)
failed to install because of missing dependencies (most of which are the other
packages that failed to install).
>     >>
>     >> R version 3.4.0 (2017-04-21)
>     >> Platform: x86_64-redhat-linux-gnu (64-bit)
>
>     > I'd make sure you have reviewed this:
>
>     > 
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essentia
> l-programs-and-libraries
>
> yes,  but see also below ..
>
>     > Best;
>     > David.
>
>     >> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
>     >>
>     >> Matrix products: default
>     >> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
>     >>
>     >> locale:
>     >> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>     >> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>     >> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>     >> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>     >> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>     >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>     >>
>     >> attached base packages:
>     >> [1] stats     graphics  grDevices utils     datasets  methods 
base
>     >>
>     >> other attached packages:
>     >> [1] dplyr_0.7.0 shiny_1.0.3
>     >>
>     >> loaded via a namespace (and not attached):
>     >> [1] compiler_3.4.0   magrittr_1.5     assertthat_0.2.0
R6_2.2.2
>     >> [5] htmltools_0.3.6  tools_3.4.0      glue_1.1.1      
tibble_1.3.3
>     >> [9] Rcpp_0.12.11     digest_0.6.12    xtable_1.8-2    
httpuv_1.3.3
>     >> [13] mime_0.5         rlang_0.1.1
>     >>>
>     >>
>     >>
>     >> If I try and install Hmisc for example I get the following
errors:
>     >> for the first error ERROR: 'configure' exists but is
not executable --
>     >> see the 'R Installation and dministration Manual'  I
did
>     >> not find the R Installation and Administration Manual
>     >> helpful.
>
> why?  It does assume you spend some time understanding what it is 
> talking about.
> OTOH, it is  *THE*  official document on the topic, written and 
> constantly updated by the  R core team.
>
> Anyway:   " ERROR: 'configure' exists but is not executable
"
>
> is I think a crucial piece of information .. it's from stringi's 
> installation failure, and the top level directory of stringi (1.1-5) 
> in a Unix like (ls -l with user group names removed) looks like:
>
>   -rw-r--r--.         1451 Apr  7 15:08 DESCRIPTION
>   -rw-r--r--.         6207 Apr  7 11:21 INSTALL
>   -rw-r--r--.         3580 Mar 21 13:29 LICENSE
>   -rw-r--r--.        63692 Apr  7 15:08 MD5
>   -rw-r--r--.         6204 Oct 24  2016 NAMESPACE
>   -rw-r--r--.        22407 Apr  7 11:44 NEWS
>   drwxr-xr-x.         8192 Mar 28 10:26 R
>   -rwxr-xr-x.           66 Apr  2  2015 cleanup
>   -rw-rw-r--.        32193 Apr  8 05:46 config.log
>   -rwxrwxr-x.        40648 Apr  8 05:46 config.status
>   -rwxr-xr-x.       173757 Apr  7 11:43 configure
>   -rw-r--r--.          669 Jun 23  2015 configure.win
>   drwxr-xr-x.          512 Apr  7 11:50 inst
>   drwxr-xr-x.         8192 Mar 28 10:26 man
>   drwxr-xr-x.        16384 Apr  8 05:47 src
>
> Note the "x"s  in the 'configure' line's "
-rwxr-xr-x. ":
> This means the file is executable and a reasonable shell can just 
> "call the file" and it will be executed, but that's the part
which
> failed for you.
>
> .. this *is* peculiar as it looks like some of the standard Unix tools 
> may be misbehaving for you .. I assume it could be some OS security 
> "feature" playing against you..
>
>     >>
>     >>
>     >>> install.packages("Hmisc")
>     >> Installing package into '/usr/lib64/R/library'
>     >> (as 'lib' is unspecified)
>     >> also installing the dependencies 'stringi',
'evaluate', 'reshape2', 'stringr', knitr',
'ggplot2', 'htmlTable', 'viridis'
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
>     >> Content type 'application/x-gzip' length 3645872 bytes
(3.5 MB)
>     >> =================================================>    
>> downloaded 3.5 MB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
>     >> Content type 'application/x-gzip' length 21914 bytes
(21 KB)
>     >> =================================================>    
>> downloaded 21 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
>     >> Content type 'application/x-gzip' length 34688 bytes
(33 KB)
>     >> =================================================>    
>> downloaded 33 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringr_1.2.0.tar.gz'
>     >> Content type 'application/x-gzip' length 94095 bytes
(91 KB)
>     >> =================================================>    
>> downloaded 91 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/knitr_1.16.tar.gz'
>     >> Content type 'application/x-gzip' length 1031259 bytes
(1007 KB)
>     >> =================================================>    
>> downloaded 1007 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz'
>     >> Content type 'application/x-gzip' length 2213308 bytes
(2.1 MB)
>     >> =================================================>    
>> downloaded 2.1 MB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/htmlTable_1.9.tar.gz'
>     >> Content type 'application/x-gzip' length 152095 bytes
(148 KB)
>     >> =================================================>    
>> downloaded 148 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz'
>     >> Content type 'application/x-gzip' length 1787731 bytes
(1.7 MB)
>     >> =================================================>    
>> downloaded 1.7 MB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/Hmisc_4.0-3.tar.gz'
>     >> Content type 'application/x-gzip' length 702759 bytes
(686 KB)
>     >> =================================================>    
>> downloaded 686 KB
>     >>
>     >> * installing *source* package 'stringi' ...
>     >> ** package 'stringi' successfully unpacked and MD5
sums checked
>     >> ERROR: 'configure' exists but is not executable -- see
the 'R Installation and dministration Manual'
>     >> * removing '/usr/lib64/R/library/stringi'
>     >> ERROR: dependency 'stringi' is not available for
package 'stringr'
>     >> * removing '/usr/lib64/R/library/stringr'
>     >> ERROR: dependency 'stringr' is not available for
package 'evaluate'
>     >> * removing '/usr/lib64/R/library/evaluate'
>     >> ERROR: dependency 'stringr' is not available for
package 'reshape2'
>     >> * removing '/usr/lib64/R/library/reshape2'
>     >> ERROR: dependencies 'evaluate', 'stringr' are
not available for package 'knitr'
>     >> * removing '/usr/lib64/R/library/knitr'
>     >> ERROR: dependency 'reshape2' is not available for
package 'ggplot2'
>     >> * removing '/usr/lib64/R/library/ggplot2'
>     >> ERROR: dependencies 'stringr', 'knitr' are not
available for package 'htmlTable
>     >> * removing '/usr/lib64/R/library/htmlTable'
>     >> ERROR: dependency 'ggplot2' is not available for
package 'viridis'
>     >> * removing '/usr/lib64/R/library/viridis'
>     >> ERROR: dependencies 'ggplot2', 'htmlTable',
'viridis' are not available for pacage 'Hmisc'
>     >> * removing '/usr/lib64/R/library/Hmisc'
>     >>
>     >>
>     >> Any help is appreciated.
>     >> --
>     >> W. Michael Conklin
>     >> Executive Vice President
>     >> Marketing & Data Sciences - North America
>     >> GfK | 8401 Golden Valley Road | Minneapolis | MN | 55427
>     >> mike.conklin at gfk.com<mailto:mike.conklin at gfk.com>
>     >> T +1 763 417 4545 | M +1 612 567 8287
>     >> www.gfk.com<http://www.gfk.com/>
>     >>
>     >>
>     >> [[alternative HTML version deleted]]
>     >>
>     >> ______________________________________________
>     >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>     >> https://stat.ethz.ch/mailman/listinfo/r-help
>     >> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>     >> and provide commented, minimal, self-contained, reproducible
code.
>
>     > David Winsemius
>     > Alameda, CA, USA
>
>     > ______________________________________________
>     > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>     > https://stat.ethz.ch/mailman/listinfo/r-help
>     > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>     > and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Conklin, Mike (GfK)

2017-Jun-22 16:00 UTC

head link

[R] Missing dependencies in pkg installs

also it seems to be no issue to execute configure from the command line 
./configure

--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK 
T +1 763 417 4545 | M +1 612 567 8287 


-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Conklin, Mike
(GfK)
Sent: Thursday, June 22, 2017 10:15 AM
To: Duncan Murdoch; Martin Maechler; David Winsemius
Cc: r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

Following Duncan's instructions I find that the system and R find that
configure IS executable but if trying to install via install.packages I get the
same error.
I also tried using R CMD INSTALL from the terminal and install.packages with a
local file pointing to the very same tar.gz file that shows the executable bit
set. All result in the same "configure is not executable" result.

[meconk at dcex1102shinypr ~]$ ls -l stringi/configure -rwxr-xr-x 1 meconk
meconk 173757 Apr  7 11:43 stringi/configure [meconk at dcex1102shinypr ~]$ sudo
R [sudo] password for meconk:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and 'citation()' on
how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]
> getwd()
[1] "/home/meconk"> file_test("-x","stringi/configure")stringi/configure
             TRUE> install.packages("stringi")                                      
Installing package into '/usr/lib64/R/library'(as 'lib' is unspecified)
trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
=================================================downloaded 3.5 MB

* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
ERROR: 'configure' exists but is not executable -- see the 'R
Installation and Administration Manual'
* removing '/usr/lib64/R/library/stringi'

The downloaded source packages are in
        '/tmp/Rtmpxw9twb/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
  installation of package 'stringi' had non-zero exit status

--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK
T +1 763 417 4545 | M +1 612 567 8287 

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Duncan
Murdoch
Sent: Thursday, June 22, 2017 8:23 AM
To: Martin Maechler; David Winsemius
Cc: r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

The "configure exists but is not executable" problem is somewhat
common on Windows, because there's usually no such thing as an executable
bit there.  (Cygwin does something to fake one, but Windows generally
doesn't.)  If you create a tarball there by default you get no executable
bits marked in it.

For a long time, R CMD build has dealt with this issue by using the internal
tar() function.  It corrects the executable bit with a warning during the build.

So if people are getting that error, something has gone wrong.  A few
guesses:

  - They are on Linux but using a mount of a Windows volume that doesn't
preserve the bit.

  - They are using a tarball produced in some strange way on Windows, e.g. by
calling tar directly instead of R CMD build.

  - There's a bug in R in detecting the executable bit.

Martin saw configure marked executable in the tarball from CRAN, which means the
second is unlikely (unless it was very recently fixed), but the first is still
possible.  One test is to manually expand the tarball, then use both ls and
R's test to see if the executable bit is set and is detected by R.  For
example, after downloading stringi_1.1.5.tar.gz you expand it using

tar zxvf stringi_1.1.5.tar.gz

and use

ls -l stringi/configure

to see if the system thinks it is executable, and in R,

file_test("-x", "stringi/configure")

to see what R sees.

Duncan Murdoch

On 22/06/2017 3:38 AM, Martin Maechler wrote:>>>>>> David Winsemius <dwinsemius at comcast.net>
>>>>>>     on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>
>     >> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)
<Mike.Conklin at gfk.com> wrote:
>     >>
>     >> I have a Ubuntu server with an R installation that has 384
packages installed.  We are trying to replicate the system on a Red Hat
Enterprise server. I downloaded the list of packages from the Ubuntu machine and
read it into an R session on the new machine. Then I ran
install.packages(listofpackages).  Now I have 352 packages on the new machine
but several very common packages (like much of the tidyverse, ggplot2, Hmisc)
failed to install because of missing dependencies (most of which are the other
packages that failed to install).
>     >>
>     >> R version 3.4.0 (2017-04-21)
>     >> Platform: x86_64-redhat-linux-gnu (64-bit)
>
>     > I'd make sure you have reviewed this:
>
>     >
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essentia
> l-programs-and-libraries
>
> yes,  but see also below ..
>
>     > Best;
>     > David.
>
>     >> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
>     >>
>     >> Matrix products: default
>     >> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
>     >>
>     >> locale:
>     >> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>     >> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>     >> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>     >> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>     >> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>     >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>     >>
>     >> attached base packages:
>     >> [1] stats     graphics  grDevices utils     datasets  methods 
base
>     >>
>     >> other attached packages:
>     >> [1] dplyr_0.7.0 shiny_1.0.3
>     >>
>     >> loaded via a namespace (and not attached):
>     >> [1] compiler_3.4.0   magrittr_1.5     assertthat_0.2.0
R6_2.2.2
>     >> [5] htmltools_0.3.6  tools_3.4.0      glue_1.1.1      
tibble_1.3.3
>     >> [9] Rcpp_0.12.11     digest_0.6.12    xtable_1.8-2    
httpuv_1.3.3
>     >> [13] mime_0.5         rlang_0.1.1
>     >>>
>     >>
>     >>
>     >> If I try and install Hmisc for example I get the following
errors:
>     >> for the first error ERROR: 'configure' exists but is
not executable --
>     >> see the 'R Installation and dministration Manual'  I
did
>     >> not find the R Installation and Administration Manual
>     >> helpful.
>
> why?  It does assume you spend some time understanding what it is 
> talking about.
> OTOH, it is  *THE*  official document on the topic, written and 
> constantly updated by the  R core team.
>
> Anyway:   " ERROR: 'configure' exists but is not executable
"
>
> is I think a crucial piece of information .. it's from stringi's 
> installation failure, and the top level directory of stringi (1.1-5) 
> in a Unix like (ls -l with user group names removed) looks like:
>
>   -rw-r--r--.         1451 Apr  7 15:08 DESCRIPTION
>   -rw-r--r--.         6207 Apr  7 11:21 INSTALL
>   -rw-r--r--.         3580 Mar 21 13:29 LICENSE
>   -rw-r--r--.        63692 Apr  7 15:08 MD5
>   -rw-r--r--.         6204 Oct 24  2016 NAMESPACE
>   -rw-r--r--.        22407 Apr  7 11:44 NEWS
>   drwxr-xr-x.         8192 Mar 28 10:26 R
>   -rwxr-xr-x.           66 Apr  2  2015 cleanup
>   -rw-rw-r--.        32193 Apr  8 05:46 config.log
>   -rwxrwxr-x.        40648 Apr  8 05:46 config.status
>   -rwxr-xr-x.       173757 Apr  7 11:43 configure
>   -rw-r--r--.          669 Jun 23  2015 configure.win
>   drwxr-xr-x.          512 Apr  7 11:50 inst
>   drwxr-xr-x.         8192 Mar 28 10:26 man
>   drwxr-xr-x.        16384 Apr  8 05:47 src
>
> Note the "x"s  in the 'configure' line's "
-rwxr-xr-x. ":
> This means the file is executable and a reasonable shell can just 
> "call the file" and it will be executed, but that's the part
which
> failed for you.
>
> .. this *is* peculiar as it looks like some of the standard Unix tools 
> may be misbehaving for you .. I assume it could be some OS security 
> "feature" playing against you..
>
>     >>
>     >>
>     >>> install.packages("Hmisc")
>     >> Installing package into '/usr/lib64/R/library'
>     >> (as 'lib' is unspecified)
>     >> also installing the dependencies 'stringi',
'evaluate', 'reshape2', 'stringr', knitr',
'ggplot2', 'htmlTable', 'viridis'
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
>     >> Content type 'application/x-gzip' length 3645872 bytes
(3.5 MB)
>     >> =================================================>    
>> downloaded 3.5 MB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
>     >> Content type 'application/x-gzip' length 21914 bytes
(21 KB)
>     >> =================================================>    
>> downloaded 21 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
>     >> Content type 'application/x-gzip' length 34688 bytes
(33 KB)
>     >> =================================================>    
>> downloaded 33 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringr_1.2.0.tar.gz'
>     >> Content type 'application/x-gzip' length 94095 bytes
(91 KB)
>     >> =================================================>    
>> downloaded 91 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/knitr_1.16.tar.gz'
>     >> Content type 'application/x-gzip' length 1031259 bytes
(1007 KB)
>     >> =================================================>    
>> downloaded 1007 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz'
>     >> Content type 'application/x-gzip' length 2213308 bytes
(2.1 MB)
>     >> =================================================>    
>> downloaded 2.1 MB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/htmlTable_1.9.tar.gz'
>     >> Content type 'application/x-gzip' length 152095 bytes
(148 KB)
>     >> =================================================>    
>> downloaded 148 KB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz'
>     >> Content type 'application/x-gzip' length 1787731 bytes
(1.7 MB)
>     >> =================================================>    
>> downloaded 1.7 MB
>     >>
>     >> trying URL
'https://cloud.r-project.org/src/contrib/Hmisc_4.0-3.tar.gz'
>     >> Content type 'application/x-gzip' length 702759 bytes
(686 KB)
>     >> =================================================>    
>> downloaded 686 KB
>     >>
>     >> * installing *source* package 'stringi' ...
>     >> ** package 'stringi' successfully unpacked and MD5
sums checked
>     >> ERROR: 'configure' exists but is not executable -- see
the 'R Installation and dministration Manual'
>     >> * removing '/usr/lib64/R/library/stringi'
>     >> ERROR: dependency 'stringi' is not available for
package 'stringr'
>     >> * removing '/usr/lib64/R/library/stringr'
>     >> ERROR: dependency 'stringr' is not available for
package 'evaluate'
>     >> * removing '/usr/lib64/R/library/evaluate'
>     >> ERROR: dependency 'stringr' is not available for
package 'reshape2'
>     >> * removing '/usr/lib64/R/library/reshape2'
>     >> ERROR: dependencies 'evaluate', 'stringr' are
not available for package 'knitr'
>     >> * removing '/usr/lib64/R/library/knitr'
>     >> ERROR: dependency 'reshape2' is not available for
package 'ggplot2'
>     >> * removing '/usr/lib64/R/library/ggplot2'
>     >> ERROR: dependencies 'stringr', 'knitr' are not
available for package 'htmlTable
>     >> * removing '/usr/lib64/R/library/htmlTable'
>     >> ERROR: dependency 'ggplot2' is not available for
package 'viridis'
>     >> * removing '/usr/lib64/R/library/viridis'
>     >> ERROR: dependencies 'ggplot2', 'htmlTable',
'viridis' are not available for pacage 'Hmisc'
>     >> * removing '/usr/lib64/R/library/Hmisc'
>     >>
>     >>
>     >> Any help is appreciated.
>     >> --
>     >> W. Michael Conklin
>     >> Executive Vice President
>     >> Marketing & Data Sciences - North America
>     >> GfK | 8401 Golden Valley Road | Minneapolis | MN | 55427
>     >> mike.conklin at gfk.com<mailto:mike.conklin at gfk.com>
>     >> T +1 763 417 4545 | M +1 612 567 8287
>     >> www.gfk.com<http://www.gfk.com/>
>     >>
>     >>
>     >> [[alternative HTML version deleted]]
>     >>
>     >> ______________________________________________
>     >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>     >> https://stat.ethz.ch/mailman/listinfo/r-help
>     >> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>     >> and provide commented, minimal, self-contained, reproducible
code.
>
>     > David Winsemius
>     > Alameda, CA, USA
>
>     > ______________________________________________
>     > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>     > https://stat.ethz.ch/mailman/listinfo/r-help
>     > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>     > and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Duncan Murdoch

2017-Jun-22 16:08 UTC

head link

[R] Missing dependencies in pkg installs

On 22/06/2017 11:15 AM, Conklin, Mike (GfK) wrote:> Following Duncan's instructions I find that the system and R find that
configure IS executable but if trying to install via install.packages I get the
same error.
> I also tried using R CMD INSTALL from the terminal and install.packages
with a local file pointing to the very same tar.gz file that shows the
executable bit set. All result in the same "configure is not
executable" result.
>
That's very mysterious.  This is hard to debug, because R runs a 
separate process to do the installs.  If you want to track this down you 
can debug the code as follows.

1.  Manually download the tarball, using any method (perhaps 
download.packages("stringi", destdir = ".", type =
"source").

2.  In R, run

debug(tools:::.install_packages)
tools:::.install_packages("stringi_1.1.5.tar.gz")

You can single step until you see the message, and try to diagnose why 
it is happening.

Watch out, this function will exit R at the end.

Duncan Murdoch
> [meconk at dcex1102shinypr ~]$ ls -l stringi/configure
> -rwxr-xr-x 1 meconk meconk 173757 Apr  7 11:43 stringi/configure
> [meconk at dcex1102shinypr ~]$ sudo R
> [sudo] password for meconk:
>
> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> [Previously saved workspace restored]
>
>> getwd()
> [1] "/home/meconk"
>> file_test("-x","stringi/configure")
> stringi/configure
>              TRUE
>> install.packages("stringi")                                  
Installing package into '/usr/lib64/R/library'
> (as 'lib' is unspecified)
> trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
> Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
> =================================================> downloaded 3.5 MB
>
> * installing *source* package 'stringi' ...
> ** package 'stringi' successfully unpacked and MD5 sums checked
> ERROR: 'configure' exists but is not executable -- see the 'R
Installation and Administration Manual'
> * removing '/usr/lib64/R/library/stringi'
>
> The downloaded source packages are in
>         '/tmp/Rtmpxw9twb/downloaded_packages'
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages("stringi") :
>   installation of package 'stringi' had non-zero exit status
>
> --
> W. Michael Conklin
> EVP Marketing & Data Sciences
> GfK
> T +1 763 417 4545 | M +1 612 567 8287
>
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Duncan
Murdoch
> Sent: Thursday, June 22, 2017 8:23 AM
> To: Martin Maechler; David Winsemius
> Cc: r-help at r-project.org
> Subject: Re: [R] Missing dependencies in pkg installs
>
> The "configure exists but is not executable" problem is somewhat
common on Windows, because there's usually no such thing as an executable
bit there.  (Cygwin does something to fake one, but Windows generally
> doesn't.)  If you create a tarball there by default you get no
executable bits marked in it.
>
> For a long time, R CMD build has dealt with this issue by using the
internal tar() function.  It corrects the executable bit with a warning during
the build.
>
> So if people are getting that error, something has gone wrong.  A few
> guesses:
>
>   - They are on Linux but using a mount of a Windows volume that
doesn't preserve the bit.
>
>   - They are using a tarball produced in some strange way on Windows, e.g.
by calling tar directly instead of R CMD build.
>
>   - There's a bug in R in detecting the executable bit.
>
> Martin saw configure marked executable in the tarball from CRAN, which
means the second is unlikely (unless it was very recently fixed), but the first
is still possible.  One test is to manually expand the tarball, then use both ls
and R's test to see if the executable bit is set and is detected by R.  For
example, after downloading stringi_1.1.5.tar.gz you expand it using
>
> tar zxvf stringi_1.1.5.tar.gz
>
> and use
>
> ls -l stringi/configure
>
> to see if the system thinks it is executable, and in R,
>
> file_test("-x", "stringi/configure")
>
> to see what R sees.
>
> Duncan Murdoch
>
> On 22/06/2017 3:38 AM, Martin Maechler wrote:
>>>>>>> David Winsemius <dwinsemius at comcast.net>
>>>>>>>     on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>>
>>     >> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)
<Mike.Conklin at gfk.com> wrote:
>>     >>
>>     >> I have a Ubuntu server with an R installation that has 384
packages installed.  We are trying to replicate the system on a Red Hat
Enterprise server. I downloaded the list of packages from the Ubuntu machine and
read it into an R session on the new machine. Then I ran
install.packages(listofpackages).  Now I have 352 packages on the new machine
but several very common packages (like much of the tidyverse, ggplot2, Hmisc)
failed to install because of missing dependencies (most of which are the other
packages that failed to install).
>>     >>
>>     >> R version 3.4.0 (2017-04-21)
>>     >> Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>>     > I'd make sure you have reviewed this:
>>
>>     >
>> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essentia
>> l-programs-and-libraries
>>
>> yes,  but see also below ..
>>
>>     > Best;
>>     > David.
>>
>>     >> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
>>     >>
>>     >> Matrix products: default
>>     >> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
>>     >>
>>     >> locale:
>>     >> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>     >> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>     >> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>     >> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>     >> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>     >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>     >>
>>     >> attached base packages:
>>     >> [1] stats     graphics  grDevices utils     datasets 
methods   base
>>     >>
>>     >> other attached packages:
>>     >> [1] dplyr_0.7.0 shiny_1.0.3
>>     >>
>>     >> loaded via a namespace (and not attached):
>>     >> [1] compiler_3.4.0   magrittr_1.5     assertthat_0.2.0
R6_2.2.2
>>     >> [5] htmltools_0.3.6  tools_3.4.0      glue_1.1.1      
tibble_1.3.3
>>     >> [9] Rcpp_0.12.11     digest_0.6.12    xtable_1.8-2    
httpuv_1.3.3
>>     >> [13] mime_0.5         rlang_0.1.1
>>     >>>
>>     >>
>>     >>
>>     >> If I try and install Hmisc for example I get the following
errors:
>>     >> for the first error ERROR: 'configure' exists but
is not executable --
>>     >> see the 'R Installation and dministration Manual' 
I did
>>     >> not find the R Installation and Administration Manual
>>     >> helpful.
>>
>> why?  It does assume you spend some time understanding what it is
>> talking about.
>> OTOH, it is  *THE*  official document on the topic, written and
>> constantly updated by the  R core team.
>>
>> Anyway:   " ERROR: 'configure' exists but is not
executable "
>>
>> is I think a crucial piece of information .. it's from
stringi's
>> installation failure, and the top level directory of stringi (1.1-5)
>> in a Unix like (ls -l with user group names removed) looks like:
>>
>>   -rw-r--r--.         1451 Apr  7 15:08 DESCRIPTION
>>   -rw-r--r--.         6207 Apr  7 11:21 INSTALL
>>   -rw-r--r--.         3580 Mar 21 13:29 LICENSE
>>   -rw-r--r--.        63692 Apr  7 15:08 MD5
>>   -rw-r--r--.         6204 Oct 24  2016 NAMESPACE
>>   -rw-r--r--.        22407 Apr  7 11:44 NEWS
>>   drwxr-xr-x.         8192 Mar 28 10:26 R
>>   -rwxr-xr-x.           66 Apr  2  2015 cleanup
>>   -rw-rw-r--.        32193 Apr  8 05:46 config.log
>>   -rwxrwxr-x.        40648 Apr  8 05:46 config.status
>>   -rwxr-xr-x.       173757 Apr  7 11:43 configure
>>   -rw-r--r--.          669 Jun 23  2015 configure.win
>>   drwxr-xr-x.          512 Apr  7 11:50 inst
>>   drwxr-xr-x.         8192 Mar 28 10:26 man
>>   drwxr-xr-x.        16384 Apr  8 05:47 src
>>
>> Note the "x"s  in the 'configure' line's "
-rwxr-xr-x. ":
>> This means the file is executable and a reasonable shell can just
>> "call the file" and it will be executed, but that's the
part which
>> failed for you.
>>
>> .. this *is* peculiar as it looks like some of the standard Unix tools
>> may be misbehaving for you .. I assume it could be some OS security
>> "feature" playing against you..
>>
>>     >>
>>     >>
>>     >>> install.packages("Hmisc")
>>     >> Installing package into '/usr/lib64/R/library'
>>     >> (as 'lib' is unspecified)
>>     >> also installing the dependencies 'stringi',
'evaluate', 'reshape2', 'stringr', knitr',
'ggplot2', 'htmlTable', 'viridis'
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
>>     >> Content type 'application/x-gzip' length 3645872
bytes (3.5 MB)
>>     >> =================================================>> 
>> downloaded 3.5 MB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
>>     >> Content type 'application/x-gzip' length 21914
bytes (21 KB)
>>     >> =================================================>> 
>> downloaded 21 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
>>     >> Content type 'application/x-gzip' length 34688
bytes (33 KB)
>>     >> =================================================>> 
>> downloaded 33 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringr_1.2.0.tar.gz'
>>     >> Content type 'application/x-gzip' length 94095
bytes (91 KB)
>>     >> =================================================>> 
>> downloaded 91 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/knitr_1.16.tar.gz'
>>     >> Content type 'application/x-gzip' length 1031259
bytes (1007 KB)
>>     >> =================================================>> 
>> downloaded 1007 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz'
>>     >> Content type 'application/x-gzip' length 2213308
bytes (2.1 MB)
>>     >> =================================================>> 
>> downloaded 2.1 MB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/htmlTable_1.9.tar.gz'
>>     >> Content type 'application/x-gzip' length 152095
bytes (148 KB)
>>     >> =================================================>> 
>> downloaded 148 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz'
>>     >> Content type 'application/x-gzip' length 1787731
bytes (1.7 MB)
>>     >> =================================================>> 
>> downloaded 1.7 MB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/Hmisc_4.0-3.tar.gz'
>>     >> Content type 'application/x-gzip' length 702759
bytes (686 KB)
>>     >> =================================================>> 
>> downloaded 686 KB
>>     >>
>>     >> * installing *source* package 'stringi' ...
>>     >> ** package 'stringi' successfully unpacked and MD5
sums checked
>>     >> ERROR: 'configure' exists but is not executable --
see the 'R Installation and dministration Manual'
>>     >> * removing '/usr/lib64/R/library/stringi'
>>     >> ERROR: dependency 'stringi' is not available for
package 'stringr'
>>     >> * removing '/usr/lib64/R/library/stringr'
>>     >> ERROR: dependency 'stringr' is not available for
package 'evaluate'
>>     >> * removing '/usr/lib64/R/library/evaluate'
>>     >> ERROR: dependency 'stringr' is not available for
package 'reshape2'
>>     >> * removing '/usr/lib64/R/library/reshape2'
>>     >> ERROR: dependencies 'evaluate', 'stringr'
are not available for package 'knitr'
>>     >> * removing '/usr/lib64/R/library/knitr'
>>     >> ERROR: dependency 'reshape2' is not available for
package 'ggplot2'
>>     >> * removing '/usr/lib64/R/library/ggplot2'
>>     >> ERROR: dependencies 'stringr', 'knitr' are
not available for package 'htmlTable
>>     >> * removing '/usr/lib64/R/library/htmlTable'
>>     >> ERROR: dependency 'ggplot2' is not available for
package 'viridis'
>>     >> * removing '/usr/lib64/R/library/viridis'
>>     >> ERROR: dependencies 'ggplot2',
'htmlTable', 'viridis' are not available for pacage
'Hmisc'
>>     >> * removing '/usr/lib64/R/library/Hmisc'
>>     >>
>>     >>
>>     >> Any help is appreciated.
>>     >> --
>>     >> W. Michael Conklin
>>     >> Executive Vice President
>>     >> Marketing & Data Sciences - North America
>>     >> GfK | 8401 Golden Valley Road | Minneapolis | MN | 55427
>>     >> mike.conklin at gfk.com<mailto:mike.conklin at
gfk.com>
>>     >> T +1 763 417 4545 | M +1 612 567 8287
>>     >> www.gfk.com<http://www.gfk.com/>
>>     >>
>>     >>
>>     >> [[alternative HTML version deleted]]
>>     >>
>>     >> ______________________________________________
>>     >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>     >> https://stat.ethz.ch/mailman/listinfo/r-help
>>     >> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>>     >> and provide commented, minimal, self-contained,
reproducible code.
>>
>>     > David Winsemius
>>     > Alameda, CA, USA
>>
>>     > ______________________________________________
>>     > R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>     > https://stat.ethz.ch/mailman/listinfo/r-help
>>     > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>>     > and provide commented, minimal, self-contained, reproducible
code.
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Conklin, Mike (GfK)

2017-Jun-22 19:42 UTC

head link

[R] Missing dependencies in pkg installs

Not much progress..... I step through debug and it gets to the do.install()
function which immediately errors with the same "configuration not
executable" error.

So, made a tempfunc that was a copy of tools:::.install_packages and edited the
file_test("-x","configure") line to return a TRUE

now I get a Permission Denied error (even if I run as root)
> tempfunc("/home/meconk/stringi_1.1.5.tar.gz")* installing to library '/usr/lib64/R/library'
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
sh: ./configure: Permission denied
ERROR: configuration failed for package 'stringi'
* removing '/usr/lib64/R/library/stringi'
Error in do_exit(status = status) : .install_packages() exit status 1
Error in do_exit(status = status) : .install_packages() exit status 1

--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK 
T +1 763 417 4545 | M +1 612 567 8287 


-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] 
Sent: Thursday, June 22, 2017 11:09 AM
To: Conklin, Mike (GfK); Martin Maechler; David Winsemius
Cc: r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs

On 22/06/2017 11:15 AM, Conklin, Mike (GfK) wrote:> Following Duncan's instructions I find that the system and R find that
configure IS executable but if trying to install via install.packages I get the
same error.
> I also tried using R CMD INSTALL from the terminal and install.packages
with a local file pointing to the very same tar.gz file that shows the
executable bit set. All result in the same "configure is not
executable" result.
>
That's very mysterious.  This is hard to debug, because R runs a separate
process to do the installs.  If you want to track this down you can debug the
code as follows.

1.  Manually download the tarball, using any method (perhaps
download.packages("stringi", destdir = ".", type =
"source").

2.  In R, run

debug(tools:::.install_packages)
tools:::.install_packages("stringi_1.1.5.tar.gz")

You can single step until you see the message, and try to diagnose why it is
happening.

Watch out, this function will exit R at the end.

Duncan Murdoch
> [meconk at dcex1102shinypr ~]$ ls -l stringi/configure -rwxr-xr-x 1 
> meconk meconk 173757 Apr  7 11:43 stringi/configure 
> [meconk at dcex1102shinypr ~]$ sudo R [sudo] password for meconk:
>
> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and 'citation()'
on how to
> cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> [Previously saved workspace restored]
>
>> getwd()
> [1] "/home/meconk"
>> file_test("-x","stringi/configure")
> stringi/configure
>              TRUE
>> install.packages("stringi")                                  
Installing package into '/usr/lib64/R/library'
> (as 'lib' is unspecified)
> trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
> Content type 'application/x-gzip' length 3645872 bytes (3.5 MB) 
> =================================================> downloaded 3.5 MB
>
> * installing *source* package 'stringi' ...
> ** package 'stringi' successfully unpacked and MD5 sums checked
> ERROR: 'configure' exists but is not executable -- see the 'R
Installation and Administration Manual'
> * removing '/usr/lib64/R/library/stringi'
>
> The downloaded source packages are in
>         '/tmp/Rtmpxw9twb/downloaded_packages'
> Updating HTML index of packages in '.Library'
> Making 'packages.html' ... done
> Warning message:
> In install.packages("stringi") :
>   installation of package 'stringi' had non-zero exit status
>
> --
> W. Michael Conklin
> EVP Marketing & Data Sciences
> GfK
> T +1 763 417 4545 | M +1 612 567 8287
>
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Duncan 
> Murdoch
> Sent: Thursday, June 22, 2017 8:23 AM
> To: Martin Maechler; David Winsemius
> Cc: r-help at r-project.org
> Subject: Re: [R] Missing dependencies in pkg installs
>
> The "configure exists but is not executable" problem is somewhat 
> common on Windows, because there's usually no such thing as an 
> executable bit there.  (Cygwin does something to fake one, but Windows 
> generally
> doesn't.)  If you create a tarball there by default you get no
executable bits marked in it.
>
> For a long time, R CMD build has dealt with this issue by using the
internal tar() function.  It corrects the executable bit with a warning during
the build.
>
> So if people are getting that error, something has gone wrong.  A few
> guesses:
>
>   - They are on Linux but using a mount of a Windows volume that
doesn't preserve the bit.
>
>   - They are using a tarball produced in some strange way on Windows, e.g.
by calling tar directly instead of R CMD build.
>
>   - There's a bug in R in detecting the executable bit.
>
> Martin saw configure marked executable in the tarball from CRAN, which 
> means the second is unlikely (unless it was very recently fixed), but 
> the first is still possible.  One test is to manually expand the 
> tarball, then use both ls and R's test to see if the executable bit is 
> set and is detected by R.  For example, after downloading 
> stringi_1.1.5.tar.gz you expand it using
>
> tar zxvf stringi_1.1.5.tar.gz
>
> and use
>
> ls -l stringi/configure
>
> to see if the system thinks it is executable, and in R,
>
> file_test("-x", "stringi/configure")
>
> to see what R sees.
>
> Duncan Murdoch
>
> On 22/06/2017 3:38 AM, Martin Maechler wrote:
>>>>>>> David Winsemius <dwinsemius at comcast.net>
>>>>>>>     on Wed, 21 Jun 2017 18:04:13 -0700 writes:
>>
>>     >> On Jun 21, 2017, at 1:39 PM, Conklin, Mike (GfK)
<Mike.Conklin at gfk.com> wrote:
>>     >>
>>     >> I have a Ubuntu server with an R installation that has 384
packages installed.  We are trying to replicate the system on a Red Hat
Enterprise server. I downloaded the list of packages from the Ubuntu machine and
read it into an R session on the new machine. Then I ran
install.packages(listofpackages).  Now I have 352 packages on the new machine
but several very common packages (like much of the tidyverse, ggplot2, Hmisc)
failed to install because of missing dependencies (most of which are the other
packages that failed to install).
>>     >>
>>     >> R version 3.4.0 (2017-04-21)
>>     >> Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>>     > I'd make sure you have reviewed this:
>>
>>     >
>> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Essenti
>> a
>> l-programs-and-libraries
>>
>> yes,  but see also below ..
>>
>>     > Best;
>>     > David.
>>
>>     >> Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
>>     >>
>>     >> Matrix products: default
>>     >> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
>>     >>
>>     >> locale:
>>     >> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>     >> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>     >> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>     >> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>     >> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>     >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>     >>
>>     >> attached base packages:
>>     >> [1] stats     graphics  grDevices utils     datasets 
methods   base
>>     >>
>>     >> other attached packages:
>>     >> [1] dplyr_0.7.0 shiny_1.0.3
>>     >>
>>     >> loaded via a namespace (and not attached):
>>     >> [1] compiler_3.4.0   magrittr_1.5     assertthat_0.2.0
R6_2.2.2
>>     >> [5] htmltools_0.3.6  tools_3.4.0      glue_1.1.1      
tibble_1.3.3
>>     >> [9] Rcpp_0.12.11     digest_0.6.12    xtable_1.8-2    
httpuv_1.3.3
>>     >> [13] mime_0.5         rlang_0.1.1
>>     >>>
>>     >>
>>     >>
>>     >> If I try and install Hmisc for example I get the following
errors:
>>     >> for the first error ERROR: 'configure' exists but
is not executable --
>>     >> see the 'R Installation and dministration Manual' 
I did
>>     >> not find the R Installation and Administration Manual
>>     >> helpful.
>>
>> why?  It does assume you spend some time understanding what it is 
>> talking about.
>> OTOH, it is  *THE*  official document on the topic, written and 
>> constantly updated by the  R core team.
>>
>> Anyway:   " ERROR: 'configure' exists but is not
executable "
>>
>> is I think a crucial piece of information .. it's from
stringi's
>> installation failure, and the top level directory of stringi (1.1-5) 
>> in a Unix like (ls -l with user group names removed) looks like:
>>
>>   -rw-r--r--.         1451 Apr  7 15:08 DESCRIPTION
>>   -rw-r--r--.         6207 Apr  7 11:21 INSTALL
>>   -rw-r--r--.         3580 Mar 21 13:29 LICENSE
>>   -rw-r--r--.        63692 Apr  7 15:08 MD5
>>   -rw-r--r--.         6204 Oct 24  2016 NAMESPACE
>>   -rw-r--r--.        22407 Apr  7 11:44 NEWS
>>   drwxr-xr-x.         8192 Mar 28 10:26 R
>>   -rwxr-xr-x.           66 Apr  2  2015 cleanup
>>   -rw-rw-r--.        32193 Apr  8 05:46 config.log
>>   -rwxrwxr-x.        40648 Apr  8 05:46 config.status
>>   -rwxr-xr-x.       173757 Apr  7 11:43 configure
>>   -rw-r--r--.          669 Jun 23  2015 configure.win
>>   drwxr-xr-x.          512 Apr  7 11:50 inst
>>   drwxr-xr-x.         8192 Mar 28 10:26 man
>>   drwxr-xr-x.        16384 Apr  8 05:47 src
>>
>> Note the "x"s  in the 'configure' line's "
-rwxr-xr-x. ":
>> This means the file is executable and a reasonable shell can just 
>> "call the file" and it will be executed, but that's the
part which
>> failed for you.
>>
>> .. this *is* peculiar as it looks like some of the standard Unix 
>> tools may be misbehaving for you .. I assume it could be some OS 
>> security "feature" playing against you..
>>
>>     >>
>>     >>
>>     >>> install.packages("Hmisc")
>>     >> Installing package into '/usr/lib64/R/library'
>>     >> (as 'lib' is unspecified)
>>     >> also installing the dependencies 'stringi',
'evaluate', 'reshape2', 'stringr', knitr',
'ggplot2', 'htmlTable', 'viridis'
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringi_1.1.5.tar.gz'
>>     >> Content type 'application/x-gzip' length 3645872
bytes (3.5 MB)
>>     >> =================================================>> 
>> downloaded 3.5 MB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/evaluate_0.10.tar.gz'
>>     >> Content type 'application/x-gzip' length 21914
bytes (21 KB)
>>     >> =================================================>> 
>> downloaded 21 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/reshape2_1.4.2.tar.gz'
>>     >> Content type 'application/x-gzip' length 34688
bytes (33 KB)
>>     >> =================================================>> 
>> downloaded 33 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/stringr_1.2.0.tar.gz'
>>     >> Content type 'application/x-gzip' length 94095
bytes (91 KB)
>>     >> =================================================>> 
>> downloaded 91 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/knitr_1.16.tar.gz'
>>     >> Content type 'application/x-gzip' length 1031259
bytes (1007 KB)
>>     >> =================================================>> 
>> downloaded 1007 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/ggplot2_2.2.1.tar.gz'
>>     >> Content type 'application/x-gzip' length 2213308
bytes (2.1 MB)
>>     >> =================================================>> 
>> downloaded 2.1 MB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/htmlTable_1.9.tar.gz'
>>     >> Content type 'application/x-gzip' length 152095
bytes (148 KB)
>>     >> =================================================>> 
>> downloaded 148 KB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/viridis_0.4.0.tar.gz'
>>     >> Content type 'application/x-gzip' length 1787731
bytes (1.7 MB)
>>     >> =================================================>> 
>> downloaded 1.7 MB
>>     >>
>>     >> trying URL
'https://cloud.r-project.org/src/contrib/Hmisc_4.0-3.tar.gz'
>>     >> Content type 'application/x-gzip' length 702759
bytes (686 KB)
>>     >> =================================================>> 
>> downloaded 686 KB
>>     >>
>>     >> * installing *source* package 'stringi' ...
>>     >> ** package 'stringi' successfully unpacked and MD5
sums checked
>>     >> ERROR: 'configure' exists but is not executable --
see the 'R Installation and dministration Manual'
>>     >> * removing '/usr/lib64/R/library/stringi'
>>     >> ERROR: dependency 'stringi' is not available for
package 'stringr'
>>     >> * removing '/usr/lib64/R/library/stringr'
>>     >> ERROR: dependency 'stringr' is not available for
package 'evaluate'
>>     >> * removing '/usr/lib64/R/library/evaluate'
>>     >> ERROR: dependency 'stringr' is not available for
package 'reshape2'
>>     >> * removing '/usr/lib64/R/library/reshape2'
>>     >> ERROR: dependencies 'evaluate', 'stringr'
are not available for package 'knitr'
>>     >> * removing '/usr/lib64/R/library/knitr'
>>     >> ERROR: dependency 'reshape2' is not available for
package 'ggplot2'
>>     >> * removing '/usr/lib64/R/library/ggplot2'
>>     >> ERROR: dependencies 'stringr', 'knitr' are
not available for package 'htmlTable
>>     >> * removing '/usr/lib64/R/library/htmlTable'
>>     >> ERROR: dependency 'ggplot2' is not available for
package 'viridis'
>>     >> * removing '/usr/lib64/R/library/viridis'
>>     >> ERROR: dependencies 'ggplot2',
'htmlTable', 'viridis' are not available for pacage
'Hmisc'
>>     >> * removing '/usr/lib64/R/library/Hmisc'
>>     >>
>>     >>
>>     >> Any help is appreciated.
>>     >> --
>>     >> W. Michael Conklin
>>     >> Executive Vice President
>>     >> Marketing & Data Sciences - North America
>>     >> GfK | 8401 Golden Valley Road | Minneapolis | MN | 55427
>>     >> mike.conklin at gfk.com<mailto:mike.conklin at
gfk.com>
>>     >> T +1 763 417 4545 | M +1 612 567 8287
>>     >> www.gfk.com<http://www.gfk.com/>
>>     >>
>>     >>
>>     >> [[alternative HTML version deleted]]
>>     >>
>>     >> ______________________________________________
>>     >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>     >> https://stat.ethz.ch/mailman/listinfo/r-help
>>     >> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>>     >> and provide commented, minimal, self-contained,
reproducible code.
>>
>>     > David Winsemius
>>     > Alameda, CA, USA
>>
>>     > ______________________________________________
>>     > R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>>     > https://stat.ethz.ch/mailman/listinfo/r-help
>>     > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>>     > and provide commented, minimal, self-contained, reproducible
code.
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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