Jay Ver Hoef - NOAA Federal
2019-Dec-11 19:29 UTC
[R-sig-Fedora] Problems with large loops in CentOS
I have run into a problem when do loops with lots of elements in CentOS (I am a new user after using Ubuntu for many years). I am attaching two scripts, one called Looping_Centos_minimal_bug_OK.R which runs fine. I simply repeat a function call in it 15 times. However, if I repeat that function call 16 times, as in this one, Looping_Centos_minimal_bug_breaks.R I get the error, Error: unexpected '}' in: "CorMod }" I have a laptop with Ubuntu installed, and everything works fine. This is just my minimal example. I have many other scripts with loops, and if they have too many functions in them, they break in CentOS, while they always work in Ubuntu. I was wondering if anyone else with CentOS or Fedora is having a similar issue, and can reproduce my problem. Thank you. Jay Ver Hoef> sessionInfo()R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /home/xverhoef/R/R-3.6.1/lib/libRblas.so LAPACK: /home/xverhoef/R/R-3.6.1/lib/libRlapack.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 R Version: platform = x86_64-pc-linux-gnu arch = x86_64 os = linux-gnu system = x86_64, linux-gnu status major = 3 minor = 6.1 year = 2019 month = 07 day = 05 svn rev = 76782 language = R version.string = R version 3.6.1 (2019-07-05) nickname = Action of the Toes Locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF- 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF- 8;LC_PAPER=en_US.UTF- 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF- 8;LC_IDENTIFICATION=C Search Path: .GlobalEnv, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, package:methods, Autoloads, package:baseR Version: platform = x86_64-pc-linux-gnu arch = x86_64 os = linux-gnu system = x86_64, linux-gnu status major = 3 minor = 6.1 year = 2019 month = 07 day = 05 svn rev = 76782 language = R version.string = R version 3.6.1 (2019-07-05) nickname = Action of the Toes Locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF- 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF- 8;LC_PAPER=en_US.UTF- 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF- 8;LC_IDENTIFICATION=C Search Path: .GlobalEnv, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, package:methods, Autoloads, package:base ************************************************************* *Jay M. Ver Hoef, Ph.D.Senior Scientist/StatisticianMarine Mammal LaboratoryNOAA-NMFS Alaska Fisheries Science CenterSeattle, WA and Fairbanks, AK, USA(907) 347-5552jay.verhoef at noaa.gov <jay.verhoef at noaa.gov> http://sites.google.com/site/jayverhoef/ <http://sites.google.com/site/jayverhoef/>* ************************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-fedora/attachments/20191211/b2e050a2/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: Looping_Centos_minimal_bug_OK.R Type: application/octet-stream Size: 4047 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-fedora/attachments/20191211/b2e050a2/attachment-0002.obj> -------------- next part -------------- A non-text attachment was scrubbed... Name: Looping_Centos_minimal_bug_breaks.R Type: application/octet-stream Size: 4200 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-fedora/attachments/20191211/b2e050a2/attachment-0003.obj>
Is this a custom build? I cannot reproduce the issue on CentOS 7 with stock R installed. I?aki On Tue, 6 Oct 2020 at 13:02, Jay Ver Hoef - NOAA Federal <jay.verhoef at noaa.gov> wrote:> > I have run into a problem when do loops with lots of elements in CentOS (I am a new user after using Ubuntu for many years). I am attaching two scripts, one called > Looping_Centos_minimal_bug_OK.R > which runs fine. I simply repeat a function call in it 15 times. However, if I repeat that function call 16 times, as in this one, > Looping_Centos_minimal_bug_breaks.R > I get the error, > Error: unexpected '}' in: > "CorMod > }" > > I have a laptop with Ubuntu installed, and everything works fine. This is just my minimal example. I have many other scripts with loops, and if they have too many functions in them, they break in CentOS, while they always work in Ubuntu. I was wondering if anyone else with CentOS or Fedora is having a similar issue, and can reproduce my problem. Thank you. > > Jay Ver Hoef > > > sessionInfo() > R version 3.6.1 (2019-07-05) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: CentOS Linux 7 (Core) > > Matrix products: default > BLAS: /home/xverhoef/R/R-3.6.1/lib/libRblas.so > LAPACK: /home/xverhoef/R/R-3.6.1/lib/libRlapack.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 > > R Version: > platform = x86_64-pc-linux-gnu > arch = x86_64 > os = linux-gnu > system = x86_64, linux-gnu > status > major = 3 > minor = 6.1 > year = 2019 > month = 07 > day = 05 > svn rev = 76782 > language = R > version.string = R version 3.6.1 (2019-07-05) > nickname = Action of the Toes > > Locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF- > 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF- > 8;LC_PAPER=en_US.UTF- > 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF- > 8;LC_IDENTIFICATION=C > > Search Path: > .GlobalEnv, package:stats, package:graphics, package:grDevices, > package:utils, package:datasets, package:methods, Autoloads, > package:baseR Version: > platform = x86_64-pc-linux-gnu > arch = x86_64 > os = linux-gnu > system = x86_64, linux-gnu > status > major = 3 > minor = 6.1 > year = 2019 > month = 07 > day = 05 > svn rev = 76782 > language = R > version.string = R version 3.6.1 (2019-07-05) > nickname = Action of the Toes > > Locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF- > 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF- > 8;LC_PAPER=en_US.UTF- > 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF- > 8;LC_IDENTIFICATION=C > > Search Path: > .GlobalEnv, package:stats, package:graphics, package:grDevices, > package:utils, package:datasets, package:methods, Autoloads, > package:base > > > > ************************************************************* > > Jay M. Ver Hoef, Ph.D. > Senior Scientist/Statistician > Marine Mammal Laboratory > NOAA-NMFS Alaska Fisheries Science Center > Seattle, WA and Fairbanks, AK, USA > (907) 347-5552 > jay.verhoef at noaa.gov > http://sites.google.com/site/jayverhoef/ > > ************************************************************* > > > _______________________________________________ > R-SIG-Fedora mailing list > R-SIG-Fedora at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora-- I?aki ?car
Hi Jay -- Works fine for me under CentOS 7 -- 16 GB RAM. The code doesn't seem to output anything, so not sure if its running 'correctly'. But, its running without error. On 12/11/2019 2:28 PM, Jay Ver Hoef - NOAA Federal wrote:> > BLAS: ? /home/xverhoef/R/R-3.6.1/lib/libRblas.so
Hi I?aki and Evan,
Thank you for checking this. My version of CentOS was installed by the
Federal Government, and there is disk encryption. I am able to regularly
update CentOS. Anyway, the problem seems to be on my end. For me, the
code just hangs... my R scripts never run if they are too long. So, I
created that script, which fails on my computer. I have a personal
computer with Ubuntu, and the same script runs fine. I am able to work
around my issues using more modular code. Thanks again.
Best Wishes,
Jay
**************************************************************Jay M. Ver
Hoef, Ph.D.Senior Scientist/StatisticianMarine Mammal LaboratoryNOAA-NMFS
Alaska Fisheries Science CenterSeattle, WA and Fairbanks, AK, USA(907)
347-5552jay.verhoef at noaa.gov <jay.verhoef at noaa.gov>
http://sites.google.com/site/jayverhoef/
<http://sites.google.com/site/jayverhoef/>**************************************************************
On Sun, Oct 11, 2020 at 9:56 AM Evan Cooch <evan.cooch at gmail.com>
wrote:
> Hi Jay --
>
> Works fine for me under CentOS 7 -- 16 GB RAM. The code doesn't seem to
> output anything, so not sure if its running 'correctly'. But, its
> running without error.
>
> On 12/11/2019 2:28 PM, Jay Ver Hoef - NOAA Federal wrote:
> >
> > BLAS: /home/xverhoef/R/R-3.6.1/lib/libRblas.so
>
>
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