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Packages with space in version number break the cache #25

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krlmlr opened this issue Jul 13, 2017 · 4 comments
Closed

Packages with space in version number break the cache #25

krlmlr opened this issue Jul 13, 2017 · 4 comments

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@krlmlr
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krlmlr commented Jul 13, 2017 •
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This likely needs to be fixed upstream (in cranlike, desc, or somewhere else), still filing here because it affects this package (and ultimately revdepcheck) and I'm not sure what the best fix is.

The reprex wipes your CRAN cache, be careful! We do seem to need a CRANCACHE_DIR env var.

library(crancache)

repos <- c(
  BioCsoft = "https://bioconductor.org/packages/3.5/bioc",
  BioCann= "https://bioconductor.org/packages/3.5/data/annotation", 
  BioCexp = "https://bioconductor.org/packages/3.5/data/experiment",
  BioCextra = "https://bioconductor.org/packages/3.5/extra", 
  CRAN = "http://cran.rstudio.com/"
)

# Caution: Wipes your CRAN cache!!!
unlink("~/.cache/R-crancache", recursive = TRUE)
install_packages("org.Hs.ipi.db", repos = repos)
#> Installing package into '/home/muelleki/R/x86_64-pc-linux-gnu-library/3.4'
#> (as 'lib' is unspecified)
#> Adding 'org.Hs.ipi.db_1.3.0.tar.gz' to the cache
#> Adding 'org.Hs.ipi.db_1.3.0_R_x86_64-pc-linux-gnu.tar.gz' to the cache
available_packages(repos = repos)
#> Error: invalid version specification '1.3.0 '
system("grep -A 10 org.Hs.ipi.db ~/.cache/R-crancache/*/*/*/PACKAGES | sed 's/$/|/'", intern = TRUE)
#>  [1] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES:Package: org.Hs.ipi.db|"                                                         
#>  [2] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES-Version: 1.3.0|"                                                                 
#>  [3] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES-Depends: R(>= 2.12.0) , methods, AnnotationDbi (>= 1.3.12), PAnnBuilder|"        
#>  [4] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES-                (>= 1.3.0)|"                                                     
#>  [5] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES-Imports: methods, AnnotationDbi, PAnnBuilder|"                                   
#>  [6] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES-License: Artistic-2.0|"                                                          
#>  [7] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES-MD5sum: bfd850aef2bda5620d7c942e90d9cc32|"                                       
#>  [8] "/home/muelleki/.cache/R-crancache/bioc-bin/src/contrib/PACKAGES:File: org.Hs.ipi.db_1.3.0_R_x86_64-pc-linux-gnu.tar.gz|"                         
#>  [9] "--|"                                                                                                                                             
#> [10] "/home/muelleki/.cache/R-crancache/bioc/src/contrib/PACKAGES:Package: org.Hs.ipi.db|"                                                             
#> [11] "/home/muelleki/.cache/R-crancache/bioc/src/contrib/PACKAGES-Version: 1.3.0 |"                                                                    
#> [12] "/home/muelleki/.cache/R-crancache/bioc/src/contrib/PACKAGES-Depends: R(>= 2.12.0) , methods, AnnotationDbi (>= 1.3.12), PAnnBuilder (>= 1.3.0) |"
#> [13] "/home/muelleki/.cache/R-crancache/bioc/src/contrib/PACKAGES-Imports: methods, AnnotationDbi, PAnnBuilder |"                                      
#> [14] "/home/muelleki/.cache/R-crancache/bioc/src/contrib/PACKAGES-License: Artistic-2.0|"                                                              
#> [15] "/home/muelleki/.cache/R-crancache/bioc/src/contrib/PACKAGES-MD5sum: 787cc8c4512e1e07c2ef0812024438ca|"                                           
#> [16] "/home/muelleki/.cache/R-crancache/bioc/src/contrib/PACKAGES:File: org.Hs.ipi.db_1.3.0.tar.gz|"
@gaborcsardi
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I think it is a bug in remotes: r-lib/remotes#73

The reprex wipes your CRAN cache, be careful! We do seem to need a CRANCACHE_DIR env var.

There is one:

crancache/R/cache-dir.R

Line 13 in ae361da

"CRANCACHE_DIR",

It should be documented, though.

@krlmlr
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krlmlr commented Jul 13, 2017

I don't think this is related to the problem in remotes, because it also occurs with the CRAN version of remotes that does not use the CRAN cache. But maybe this means we just need to fix desc? (Or is it fixed there already?)

library(crancache)

repos <- c(
  BioCsoft = "https://bioconductor.org/packages/3.5/bioc",
  BioCann= "https://bioconductor.org/packages/3.5/data/annotation", 
  BioCexp = "https://bioconductor.org/packages/3.5/data/experiment",
  BioCextra = "https://bioconductor.org/packages/3.5/extra", 
  CRAN ="http://cran.rstudio.com/"
)

tempdir <- tempfile("R-crancache")
dir.create(tempdir)

withr::with_envvar(
  c(CRANCACHE_DIR = tempdir),
  {
    install_packages("org.Hs.ipi.db", repos = repos)
    available_packages(repos = repos)
  }
)
#> Installing package into '/home/muelleki/R/x86_64-pc-linux-gnu-library/3.4'
#> (as 'lib' is unspecified)
#> Adding 'org.Hs.ipi.db_1.3.0.tar.gz' to the cache
#> Adding 'org.Hs.ipi.db_1.3.0_R_x86_64-pc-linux-gnu.tar.gz' to the cache
#> Error: invalid version specification '1.3.0 '
Session info 
devtools::session_info()
#> Session info -------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.4.1 (2017-06-30)
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_US:en                    
#>  collate  en_US.UTF-8                 
#>  tz       Europe/Busingen             
#>  date     2017-07-13
#> Packages -----------------------------------------------------------------
#>  package    * version    date       source                             
#>  assertthat   0.2.0      2017-04-11 CRAN (R 3.4.1)                     
#>  backports    1.1.0      2017-05-22 CRAN (R 3.4.1)                     
#>  base       * 3.4.1      2017-07-08 local                              
#>  bit          1.1-12     2014-04-09 CRAN (R 3.4.0)                     
#>  bit64        0.9-8      2017-06-10 R-Forge (R 3.4.0)                  
#>  blob         1.1.0      2017-06-17 CRAN (R 3.4.1)                     
#>  callr        1.0.0.9000 2017-07-10 Github (r-lib/callr@ce3f15c)       
#>  compiler     3.4.1      2017-07-08 local                              
#>  crancache  * 0.0.0.9000 2017-07-13 local                              
#>  cranlike     1.0.0      2017-07-11 local                              
#>  crayon       1.3.2.9000 2017-07-10 Github (gaborcsardi/crayon@750190f)
#>  curl         2.7        2017-06-26 CRAN (R 3.4.1)                     
#>  datasets   * 3.4.1      2017-07-08 local                              
#>  DBI          0.7        2017-06-18 CRAN (R 3.4.1)                     
#>  debugme      1.0.2      2017-03-01 CRAN (R 3.4.1)                     
#>  desc         1.1.0      2017-01-27 CRAN (R 3.4.1)                     
#>  devtools     1.13.2     2017-06-02 CRAN (R 3.4.1)                     
#>  digest       0.6.12     2017-01-27 CRAN (R 3.4.1)                     
#>  evaluate     0.10.1     2017-06-24 CRAN (R 3.4.1)                     
#>  graphics   * 3.4.1      2017-07-08 local                              
#>  grDevices  * 3.4.1      2017-07-08 local                              
#>  htmltools    0.3.6      2017-04-28 CRAN (R 3.4.1)                     
#>  knitr        1.16       2017-05-18 CRAN (R 3.4.1)                     
#>  magrittr     1.5        2014-11-22 CRAN (R 3.4.1)                     
#>  memoise      1.1.0      2017-04-21 CRAN (R 3.4.0)                     
#>  methods    * 3.4.1      2017-07-08 local                              
#>  parsedate    1.1.3      2017-03-02 CRAN (R 3.4.0)                     
#>  pkgconfig    2.0.1      2017-03-21 CRAN (R 3.4.1)                     
#>  processx     2.0.1      2017-07-10 Github (r-lib/processx@4bf780f)    
#>  R6           2.2.2      2017-06-17 CRAN (R 3.4.1)                     
#>  rappdirs     0.3.1      2016-03-28 CRAN (R 3.4.0)                     
#>  Rcpp         0.12.11    2017-05-22 CRAN (R 3.4.1)                     
#>  rlang        0.1.1      2017-05-18 CRAN (R 3.4.1)                     
#>  rmarkdown    1.6        2017-06-15 CRAN (R 3.4.1)                     
#>  rprojroot    1.2        2017-01-16 CRAN (R 3.4.1)                     
#>  RSQLite      2.0        2017-07-09 Github (rstats-db/RSQLite@88c7c64) 
#>  rstudioapi   0.6        2016-06-27 CRAN (R 3.4.1)                     
#>  stats      * 3.4.1      2017-07-08 local                              
#>  stringi      1.1.5      2017-04-07 CRAN (R 3.4.1)                     
#>  stringr      1.2.0      2017-02-18 CRAN (R 3.4.1)                     
#>  tibble       1.3.3      2017-05-28 CRAN (R 3.4.1)                     
#>  tools        3.4.1      2017-07-08 local                              
#>  utils      * 3.4.1      2017-07-08 local                              
#>  withr        1.0.2      2016-06-20 CRAN (R 3.4.1)                     
#>  yaml         2.1.14     2016-11-12 CRAN (R 3.4.1)

@krlmlr
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krlmlr commented Jul 13, 2017

FWIW, desc also struggles with this:

desc::desc_get_version("/home/muelleki/.cache/R-crancache/bioc/src/contrib/org.Hs.ipi.db/DESCRIPTION")
#> Error: invalid version specification '1.3.0 '

@krlmlr krlmlr mentioned this issue Jul 13, 2017
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gaborcsardi added a commit to r-hub/cranlike that referenced this issue Aug 3, 2017
@gaborcsardi
Fix pkgs with trailing whitespace in version
62b5d82 
We trim the whitespace now, because it causes
problems in downstream tools:
r-lib/crancache#25
@gaborcsardi
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Fixed now in cranlike, we just trim the whitespace before creating PACKAGES*: r-hub/cranlike@62b5d82

@gaborcsardi gaborcsardi mentioned this issue Oct 19, 2017
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