[R] Corrupted package?
Patrick Connolly
p_conno||y @end|ng |rom @||ng@hot@co@nz
Thu Nov 1 08:51:05 CET 2018
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
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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