I got this message while using a dplyr mutate call: Error in get0(oNam, envir = ns) : lazy-load database '/home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb' is corrupt I had only just installed R-3.5.1 and updated the packages (using the function update.packages with the checkBuild parameter to TRUE) in the library I use with that version. So, I checked the size of pkgconfig.rdb with the previous version from the bash prompt:> ll `locate pkgconfig.rdb`-rw-r--r-- 1 hrapgc hrapgc 5335 May 8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 15669 May 8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/R/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 5359 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 4367 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb While the pkgconfig.rdb filesize in the help directory is nearly identical in size to that in R-3.5.0 (and previous versions) the one in the R directory is very much smaller. So the error message probably makes sense. The question is: how could that have happened? I removed the package and reinstalled it, but that made no difference. Is this documented anywhere? TIA -- ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. ___ Patrick Connolly {~._.~} Great minds discuss ideas _( Y )_ Average minds discuss events (:_~*~_:) Small minds discuss people (_)-(_) ..... Eleanor Roosevelt ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
Hm, a source install to r-devel gave me
Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/R/pkgconfig.rdb
-rw-r--r-- 1 pd staff 4515 Oct 31 19:15 library/pkgconfig/R/pkgconfig.rdb
Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/help/pkgconfig.rdb
-rw-r--r-- 1 pd staff 5748 Oct 31 19:15 library/pkgconfig/help/pkgconfig.rdb
and an install to R_3.4.1 (yes, 4...) said
$ ls -l
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/*/pkgconfig.rdb
-rw-r--r-- 1 pd admin 2432 Aug 17 11:36
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/R/pkgconfig.rdb
-rw-r--r-- 1 pd admin 5412 Aug 17 11:36
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/help/pkgconfig.rdb
I.e., it looks like it is the larger of your file sizes that is anomalous(?).
Did you try a straight install with install.packages("pkgconfig")?
And, BTW, which system are you using?
-pd
> On 31 Oct 2018, at 08:22 , Patrick Connolly <p_connolly at
slingshot.co.nz> wrote:
>
>
> I got this message while using a dplyr mutate call:
>
> Error in get0(oNam, envir = ns) :
> lazy-load database
'/home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb' is
corrupt
>
> I had only just installed R-3.5.1 and updated the packages (using the
> function update.packages with the checkBuild parameter to TRUE) in the
> library I use with that version. So, I checked the size of
> pkgconfig.rdb with the previous version from the bash prompt:
>
>> ll `locate pkgconfig.rdb`
>
> -rw-r--r-- 1 hrapgc hrapgc 5335 May 8 14:06
/home/hrapgc/local/R-3.5.0/library/pkgconfig/help/pkgconfig.rdb
> -rw-r--r-- 1 hrapgc hrapgc 15669 May 8 14:06
/home/hrapgc/local/R-3.5.0/library/pkgconfig/R/pkgconfig.rdb
> -rw-r--r-- 1 hrapgc hrapgc 5359 Oct 31 16:12
/home/hrapgc/local/R-3.5.1/library/pkgconfig/help/pkgconfig.rdb
> -rw-r--r-- 1 hrapgc hrapgc 4367 Oct 31 16:12
/home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb
>
> While the pkgconfig.rdb filesize in the help directory is nearly
> identical in size to that in R-3.5.0 (and previous versions) the one
> in the R directory is very much smaller. So the error message
> probably makes sense.
>
> The question is: how could that have happened? I removed the package
> and reinstalled it, but that made no difference. Is this documented
> anywhere?
>
> TIA
> --
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
> ___ Patrick Connolly
> {~._.~} Great minds discuss ideas
> _( Y )_ Average minds discuss events
> (:_~*~_:) Small minds discuss people
> (_)-(_) ..... Eleanor Roosevelt
>
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>
> ______________________________________________
> 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.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
> On Oct 31, 2018, at 11:30 AM, peter dalgaard <pdalgd at gmail.com> wrote: > > Hm, a source install to r-devel gave me > > Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/R/pkgconfig.rdb > -rw-r--r-- 1 pd staff 4515 Oct 31 19:15 library/pkgconfig/R/pkgconfig.rdb > Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/help/pkgconfig.rdb > -rw-r--r-- 1 pd staff 5748 Oct 31 19:15 library/pkgconfig/help/pkgconfig.rdb > > and an install to R_3.4.1 (yes, 4...) said > > $ ls -l /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/*/pkgconfig.rdb > -rw-r--r-- 1 pd admin 2432 Aug 17 11:36 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/R/pkgconfig.rdb > -rw-r--r-- 1 pd admin 5412 Aug 17 11:36 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/help/pkgconfig.rdb > > I.e., it looks like it is the larger of your file sizes that is anomalous(?). > > Did you try a straight install with install.packages("pkgconfig")? > > And, BTW, which system are you using? > > -pd > >> On 31 Oct 2018, at 08:22 , Patrick Connolly <p_connolly at slingshot.co.nz> wrote: >> >> >> I got this message while using a dplyr mutate call: >> >> Error in get0(oNam, envir = ns) : >> lazy-load database '/home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb' is corrupt >> >> I had only just installed R-3.5.1 and updated the packages (using the >> function update.packages with the checkBuild parameter to TRUE) in theDid you misspell "checkBuilt"? You should always present the transcript to prevent such questions. -- David.>> library I use with that version. So, I checked the size of >> pkgconfig.rdb with the previous version from the bash prompt: >> >>> ll `locate pkgconfig.rdb` >> >> -rw-r--r-- 1 hrapgc hrapgc 5335 May 8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/help/pkgconfig.rdb >> -rw-r--r-- 1 hrapgc hrapgc 15669 May 8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/R/pkgconfig.rdb >> -rw-r--r-- 1 hrapgc hrapgc 5359 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/help/pkgconfig.rdb >> -rw-r--r-- 1 hrapgc hrapgc 4367 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb >> >> While the pkgconfig.rdb filesize in the help directory is nearly >> identical in size to that in R-3.5.0 (and previous versions) the one >> in the R directory is very much smaller. So the error message >> probably makes sense. >> >> The question is: how could that have happened? I removed the package >> and reinstalled it, but that made no difference. Is this documented >> anywhere? >> >> TIA >> -- >> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. >> ___ Patrick Connolly >> {~._.~} Great minds discuss ideas >> _( Y )_ Average minds discuss events >> (:_~*~_:) Small minds discuss people >> (_)-(_) ..... Eleanor Roosevelt >> >> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. >> >> ______________________________________________ >> 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. > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com > > ______________________________________________ > 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.
On Wed, 31-Oct-2018 at 07:30PM +0100, peter dalgaard wrote: |> Hm, a source install to r-devel gave me |> |> Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/R/pkgconfig.rdb |> -rw-r--r-- 1 pd staff 4515 Oct 31 19:15 library/pkgconfig/R/pkgconfig.rdb |> Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/help/pkgconfig.rdb |> -rw-r--r-- 1 pd staff 5748 Oct 31 19:15 library/pkgconfig/help/pkgconfig.rdb |> |> and an install to R_3.4.1 (yes, 4...) said |> |> $ ls -l /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/*/pkgconfig.rdb |> -rw-r--r-- 1 pd admin 2432 Aug 17 11:36 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/R/pkgconfig.rdb |> -rw-r--r-- 1 pd admin 5412 Aug 17 11:36 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/help/pkgconfig.rdb |> |> I.e., it looks like it is the larger of your file sizes that is anomalous(?). |> That's very strange. If I look further back, the large size is historical in my experience. ll `locate pkgconfig.rdb` -rw-r--r-- 1 hrapgc hrapgc 5356 Aug 8 2017 /home/hrapgc/local/R-3.4.4/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 13377 Aug 8 2017 /home/hrapgc/local/R-3.4.4/library/pkgconfig/R/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 5335 May 8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 15669 May 8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/R/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 5359 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 hrapgc hrapgc 4367 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb Yet when I look at my home machine that I use sometimes:> ll `locate pkgconfig.rdb`-rw-r--r-- 1 pat pat 5349 Sep 13 2017 /home/pat/local/R-3.2.3/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 pat pat 13374 Sep 13 2017 /home/pat/local/R-3.2.3/library/pkgconfig/R/pkgconfig.rdb -rw-r--r-- 1 pat pat 5355 Feb 2 2018 /home/pat/local/R-3.4.3/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 pat pat 13392 Feb 2 2018 /home/pat/local/R-3.4.3/library/pkgconfig/R/pkgconfig.rdb -rw-r--r-- 1 pat pat 5356 Apr 13 2018 /home/pat/local/R-3.4.4/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 pat pat 13392 Apr 13 2018 /home/pat/local/R-3.4.4/library/pkgconfig/R/pkgconfig.rdb -rw-r--r-- 1 pat pat 5351 Jul 3 20:38 /home/pat/local/R-3.5.0/library/pkgconfig/help/pkgconfig.rdb -rw-r--r-- 1 pat pat 4349 Jul 3 20:38 /home/pat/local/R-3.5.0/library/pkgconfig/R/pkgconfig.rdb Similar sizes, but not corresponding to the same R versions!! |> Did you try a straight install with install.packages("pkgconfig")? Another interesting story:> install.packages("pkgconfig")trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/pkgconfig_2.0.2.tar.gz' Content type 'application/x-gzip' length 6024 bytes =================================================downloaded 6024 bytes This session PID is 24632: begun at 2018-11-01 11:11:41: * installing *source* package ?pkgconfig? ... ** package ?pkgconfig? successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading Error in unloadNamespace(pkg_name) : namespace ?pkgconfig? is imported by ?dplyr? so cannot be unloaded * removing ?/home/hrapgc/local/R-3.5.1/library/pkgconfig? * restoring previous ?/home/hrapgc/local/R-3.5.1/library/pkgconfig? The downloaded source packages are in ?/tmp/RtmpQ3KfLM/downloaded_packages? Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("pkgconfig") : installation of package ?pkgconfig? had non-zero exit status ---- So I used this approach: echo 'options(repos=list(CRAN="https://cloud.r-project.org"));install.packages("pkgconfig", depend = TRUE)' | R --vanilla That was "successful", even if corrupted. |> |> And, BTW, which system are you using? |>> sessionInfo()R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /home/hrapgc/local/R-3.5.1/lib/libRblas.so LAPACK: /home/hrapgc/local/R-3.5.1/lib/libRlapack.so locale: [1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_NZ.UTF-8 [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8 [7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grDevices utils stats graphics methods base other attached packages: ## <probably unnecessary detail> [1] bindrcpp_0.2.2 ggthemes_4.0.1 cowplot_0.9.3 ggrepel_0.8.0 [5] quanteda_1.3.4 topicmodels_0.2-7 rvest_0.3.2 xml2_1.2.0 [9] wordcloud_2.6 RColorBrewer_1.1-2 wordcloud2_0.2.1 tm_0.7-5 [13] NLP_0.2-0 tidytext_0.2.0 forcats_0.3.0 stringr_1.3.1 [17] purrr_0.2.5 readr_1.1.1 tidyr_0.8.2 tibble_1.4.2 [21] ggplot2_3.1.0 tidyverse_1.2.1 knitr_1.20 slam_0.1-43 [25] RcppParallel_4.4.1 tokenizers_0.2.1 dplyr_0.7.7 lattice_0.20-35 loaded via a namespace (and not attached): [1] Rcpp_0.12.19 here_0.1 lubridate_1.7.4 rprojroot_1.3-2 [5] assertthat_0.2.0 digest_0.6.18 R6_2.3.0 cellranger_1.1.0 [9] plyr_1.8.4 backports_1.1.2 stats4_3.5.1 httr_1.3.1 [13] pillar_1.3.0 rlang_0.3.0.1 curl_3.2 lazyeval_0.2.1 [17] readxl_1.1.0 rstudioapi_0.8 data.table_1.11.8 Matrix_1.2-14 [21] selectr_0.4-1 htmlwidgets_1.3 munsell_0.5.0 broom_0.5.0 [25] compiler_3.5.1 janeaustenr_0.1.5 spacyr_0.9.91 modelr_0.1.2 [29] pkgconfig_2.0.2 htmltools_0.3.6 tidyselect_0.2.5 crayon_1.3.4 [33] withr_2.1.2 SnowballC_0.5.1 grid_3.5.1 nlme_3.1-137 [37] jsonlite_1.5 gtable_0.2.0 magrittr_1.5 scales_1.0.0 [41] cli_1.0.1 stringi_1.2.4 stopwords_0.9.0 fastmatch_1.1-0 [45] tools_3.5.1 glue_1.3.0 hms_0.4.2 parallel_3.5.1 [49] colorspace_1.3-2 bindr_0.1.1 haven_1.1.2 modeltools_0.2-22></probably unnecessary detail> |> -pd |> [..] -- ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. ___ Patrick Connolly {~._.~} Great minds discuss ideas _( Y )_ Average minds discuss events (:_~*~_:) Small minds discuss people (_)-(_) ..... Eleanor Roosevelt ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.