Can't Load R DESeq2 Library, Installed All Missing Packages and Still Have Problems

Question

I'm running into some bad problems installing and using the DESeq2 package for R.

I freshly installed R 3.3.1 and Rstudio 0.99.903 on Win7. I tried installing DESeq2 using:

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

but it run into a lot of errors (some missing packages for some dependency packages etc...) Then I tried installing all the missing packages manually by downloading from CREN and installing the missing packages from .zip files.

Then I tried running few commands and I hope the information from them will help finding the cause of all the errors: First the biocLite (the installer of all the related packages, on the previous installation of the DESeq2 package everything was smooth... but it was on Linux)

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'survival'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
              binary source needs_compilation
GenomicRanges 1.24.2 1.24.3              TRUE

  Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘lattice’ ‘mgcv’ ‘survival’
  These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'survival'
Update all/some/none? [a/s/n]: 
n
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘DESeq2’
also installing the dependency ‘Rcpp’


  There is a binary version available but the source version is later:
       binary source needs_compilation
Rcpp 0.12.4.5 0.12.7              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/DESeq2_1.12.4.zip'
Content type 'application/zip' length 3937521 bytes (3.8 MB)
downloaded 3.8 MB

package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'Rcpp', 'survival'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
                binary source needs_compilation
GenomicRanges   1.24.2 1.24.3              TRUE
Rcpp          0.12.4.5 0.12.7              TRUE

  Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘lattice’ ‘mgcv’ ‘survival’
  These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB

trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages

Then trying to install the DESeq2 package with biocLite (looks like everything is good)

> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘DESeq2’
also installing the dependency ‘Rcpp’


  There is a binary version available but the source version is later:
       binary source needs_compilation
Rcpp 0.12.4.5 0.12.7              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/DESeq2_1.12.4.zip'
Content type 'application/zip' length 3937521 bytes (3.8 MB)
downloaded 3.8 MB

package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages
Old packages: 'GenomicRanges', 'lattice', 'mgcv', 'Rcpp', 'survival'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
                binary source needs_compilation
GenomicRanges   1.24.2 1.24.3              TRUE
Rcpp          0.12.4.5 0.12.7              TRUE

  Binaries will be installed
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘lattice’ ‘mgcv’ ‘survival’
  These will not be installed
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/GenomicRanges_1.24.2.zip'
Content type 'application/zip' length 2723057 bytes (2.6 MB)
downloaded 2.6 MB

trying URL 'https://bioconductor.org/packages/3.3/extra/bin/windows/contrib/3.3/Rcpp_0.12.4.5.zip'
Content type 'application/zip' length 6458713 bytes (6.2 MB)
downloaded 6.2 MB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages 

Now loading the DESeq2 library (Errors...):

> library("DESeq2")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unsplit


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘data.table’
Error: package or namespace load failed for ‘DESeq2’

Tried installing the missing package:

> install.packages('data.table', dependencies = TRUE)
also installing the dependencies ‘minqa’, ‘nloptr’, ‘RcppEigen’, ‘lme4’, ‘SparseM’, ‘pbkrtest’, ‘quantreg’, ‘mime’, ‘bit’, ‘gtools’, ‘car’, ‘markdown’, ‘yaml’, ‘bdsmatrix’, ‘sandwich’, ‘lmtest’, ‘chron’, ‘testthat’, ‘hexbin’, ‘fastmatch’, ‘xts’, ‘bit64’, ‘gdata’, ‘caret’, ‘knitr’, ‘curl’, ‘zoo’, ‘plm’

Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘minqa’ ‘nloptr’ ‘RcppEigen’ ‘lme4’ ‘SparseM’ ‘quantreg’ ‘mime’ ‘bit’ ‘gtools’ ‘markdown’
  ‘yaml’ ‘bdsmatrix’ ‘lmtest’ ‘chron’ ‘testthat’ ‘hexbin’ ‘fastmatch’ ‘xts’ ‘bit64’ ‘caret’
  ‘curl’ ‘zoo’ ‘data.table’
  These will not be installed
installing the source packages ‘pbkrtest’, ‘car’, ‘sandwich’, ‘gdata’, ‘knitr’, ‘plm’

trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-6.tar.gz'
Content type 'application/x-gzip' length 165269 bytes (161 KB)
downloaded 161 KB

trying URL 'https://cran.rstudio.com/src/contrib/car_2.1-3.tar.gz'
Content type 'application/x-gzip' length 622922 bytes (608 KB)
downloaded 608 KB

trying URL 'https://cran.rstudio.com/src/contrib/sandwich_2.3-4.tar.gz'
Content type 'application/x-gzip' length 466729 bytes (455 KB)
downloaded 455 KB

trying URL 'https://cran.rstudio.com/src/contrib/gdata_2.17.0.tar.gz'
Content type 'application/x-gzip' length 1041264 bytes (1016 KB)
downloaded 1016 KB

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.14.tar.gz'
Content type 'application/x-gzip' length 1017858 bytes (994 KB)
downloaded 994 KB

trying URL 'https://cran.rstudio.com/src/contrib/plm_1.5-12.tar.gz'
Content type 'application/x-gzip' length 1246790 bytes (1.2 MB)
downloaded 1.2 MB

ERROR: dependency 'lme4' is not available for package 'pbkrtest'
* removing 'C:/Program Files/R/R-3.3.1/library/pbkrtest'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/pbkrtest_0.4-6.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency 'zoo' is not available for package 'sandwich'
* removing 'C:/Program Files/R/R-3.3.1/library/sandwich'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/sandwich_2.3-4.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘sandwich’ had non-zero exit status
ERROR: dependency 'gtools' is not available for package 'gdata'
* removing 'C:/Program Files/R/R-3.3.1/library/gdata'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/gdata_2.17.0.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘gdata’ had non-zero exit status
ERROR: dependencies 'markdown', 'yaml' are not available for package 'knitr'
* removing 'C:/Program Files/R/R-3.3.1/library/knitr'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/knitr_1.14.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘knitr’ had non-zero exit status
ERROR: dependencies 'pbkrtest', 'quantreg' are not available for package 'car'
* removing 'C:/Program Files/R/R-3.3.1/library/car'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/car_2.1-3.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status
ERROR: dependencies 'bdsmatrix', 'zoo', 'sandwich', 'car', 'lmtest' are not available for package 'plm'
* removing 'C:/Program Files/R/R-3.3.1/library/plm'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.1\library" C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC/downloaded_packages/plm_1.5-12.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘plm’ had non-zero exit status

The downloaded source packages are in
    ‘C:\Users\user\AppData\Local\Temp\Rtmp0wyDJC\downloaded_packages’

And sessioninfo:

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255    LC_MONETARY=Hebrew_Israel.1255
[4] LC_NUMERIC=C                   LC_TIME=Hebrew_Israel.1255    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SummarizedExperiment_1.2.3 Biobase_2.32.0             GenomicRanges_1.24.2      
[4] GenomeInfoDb_1.8.7         IRanges_2.6.1              S4Vectors_0.10.3          
[7] BiocGenerics_0.18.0        BiocInstaller_1.22.3      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.4.5       Formula_1.2-1       cluster_2.0.4       XVector_0.12.1      splines_3.3.1      
 [6] zlibbioc_1.18.0     munsell_0.4.3       BiocParallel_1.6.6  colorspace_1.2-6    lattice_0.20-33    
[11] plyr_1.8.4          tools_3.3.1         nnet_7.3-12         grid_3.3.1          gtable_0.2.0       
[16] latticeExtra_0.6-28 survival_2.39-4     Matrix_1.2-7.1      gridExtra_2.2.1     RColorBrewer_1.1-2 
[21] ggplot2_2.1.0       acepack_1.3-3.3     rpart_4.1-10        scales_0.4.0        foreign_0.8-66     
> 

Because I already installed >10 packages by hand I assume the solution is not to keep installing the missing packages because those packages will have more missing packages and more and more and I won't get out of this loop.

I also tried something I found on google:

remove.packages(c("ggplot2", "data.table"))
install.packages('Rcpp', dependencies = TRUE)
install.packages('ggplot2', dependencies = TRUE)

but the installation had errors too, I can write them here if needed.

I hope you can see something I can't see and help me solving this issue.

Thanks.

Answer 1

It seems that lots of packages, most importantly data.table and lme4, were not properly compiled.

I would suggest to install data.table, lme4 and all of the packages denoted in the 2 statements that said Packages which are only available in source form, and may need compilation of C/C++/Fortran: with pacman then re-run the Bioconductor installation of your target package.

install.packages("pacman")
pacman::p_load(data.table, lme4, lattice, mgcv, survival, zoo, markdown,... <etc>)
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

I just confirmed this works on Windows.

Also note, however, that the error you got has been associated in the past with mirror outages. So if you still get this error try changing your CRAN mirror. install.packages('<package_name>', repo='http://nbcgib.uesc.br/mirrors/cran/')

Also make sure that you have RTools.exe installed and working.

Answer 2

biocLite(), install.packages() (and the devtools equivalent?) check that immediate dependencies are installed, but not that the dependencies of those, etc are installed. Likely what happened is that you managed to install a dependency, but then corrupted your installation by removing one of it's dependencies (manually via remove.packages(), or changing .libPaths(), or...? it would be good to hear any speculation you have of how this might have happened).

One solution is to find all available packages

avail = available.packages(repos=BiocInstaller::biocinstallRepos())

then all dependencies

deps0 = tools::package_depenencies("DESeq2", avail)
deps = unique(unlist(deps0, use.names=FALSE))

and unsatisfied dependencies

need = setdiff(deps, rownames(installed.packages()))

I'd take a look at need, to see if there are any insights to be had, so that you can correct the root problem rather than having to do this procedure with other packages. And finally, install the problem packages, perhaps also DESeq2.

biocLite(c(need, "DESeq2"))

In the Bioconductor realm, I would then check that package versions are consistent with the version of Bioconductor in use

BiocInstaller::biocValid()

and would ask more Bioconductor-related questions on the Bioconductor support site

Answer 3

This is the same answer I wrote in a comment to Hack-R I just wanted to post a separate answer:

What I did was - uninstalled everything (RTools then RStudio thenR and also I deleted the R directory because it still had all the previous libraries) I did this in order to eliminate any chance that something was corrupt.

(I highlighted the important points):

Then I reinstalled R then Rstudio then RTools. I again tried the installation with biocLite but was met with errors of missing packages (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors) so I changed the CRAN mirror in RStudio. I tried the installation with biocLite again and was met with missing packages again (or the installation was ok and the when I tried loading the DESeq2 library I was met with missing packages errors, I don't remember) BUT!!! now when I tried installing the missing packages manually (with install.packages("missingPackage")) they did install correctly. Finally After 3-4 manual installations of missing packages everything worked.

Sorry for the mediocre English.

I hope I helped somebody.

Answer 4

Try the following

if(! "pacman" %in% installed.packages()) install.packages("pacman")    

pacman::p_load(char = packages)

pacman::p_load(DESeq2)

install.packages("DESeq2")

library("DESeq2")