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Question: Unable to load library DESeq2 (installation of package had non-zero exit status)
1
gravatar for CandiceChuDVM
28 days ago by
CandiceChuDVM30 wrote:

I was unable to load DESeq2 this morning. I have tried to uninstall R and R Studio then reinstall them, but I still got the same warning when running library(DESeq2):

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

I have tried install.packages("bit") This is what I got:

> install.packages("bit")


  There is a binary version available but the source version is later:

    binary source needs_compilation

bit 1.1-12 1.1-13              TRUE


Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes

installing the source package ‘bit’


trying URL 'https://cran.rstudio.com/src/contrib/bit_1.1-13.tar.gz'

Content type 'application/x-gzip' length 54723 bytes (53 KB)

==================================================

downloaded 53 KB


* installing *source* package ‘bit’ ...

** package ‘bit’ successfully unpacked and MD5 sums checked

** libs

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

ERROR: compilation failed for package ‘bit’

* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/bit’

Warning in install.packages :

  installation of package ‘bit’ had non-zero exit status


The downloaded source packages are in

‘/private/var/folders/x7/cl6c9fjs0mq8k2lnrw7ls6q40000gn/T/RtmpLbCPrO/downloaded_packages’

Alternatively, I've tried biocLite("bit")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).

Installing package(s) ‘bit’


  There is a binary version available but the source version is later:

    binary source needs_compilation

bit 1.1-12 1.1-13              TRUE


Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes

installing the source package ‘bit’


trying URL 'https://cran.rstudio.com/src/contrib/bit_1.1-13.tar.gz'

Content type 'application/x-gzip' length 54723 bytes (53 KB)

==================================================

downloaded 53 KB


* installing *source* package ‘bit’ ...

** package ‘bit’ successfully unpacked and MD5 sums checked

** libs

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

ERROR: compilation failed for package ‘bit’

* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/bit’


The downloaded source packages are in

‘/private/var/folders/x7/cl6c9fjs0mq8k2lnrw7ls6q40000gn/T/RtmpLbCPrO/downloaded_packages’

Old packages: 'RcppArmadillo'

Update all/some/none? [a/s/n]: 

If answering a, I will be lead to here:

There is a binary version available but the source version is later:
                   binary    source needs_compilation
RcppArmadillo 0.8.400.0.0 0.8.500.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) 

If answering yes, I would have received the same warning:

Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘bit’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘RcppArmadillo’ had non-zero exit status

Does anyone know how to solve the problem?

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] SummarizedExperiment_1.10.1 DelayedArray_0.6.0         
 [3] BiocParallel_1.14.1         matrixStats_0.53.1         
 [5] Biobase_2.40.0              GenomicRanges_1.32.3       
 [7] GenomeInfoDb_1.16.0         IRanges_2.14.10            
 [9] S4Vectors_0.18.2            BiocGenerics_0.26.0        
[11] BiocInstaller_1.30.0        RcppArmadillo_0.8.400.0.0  
[13] ggplot2_2.2.1              

loaded via a namespace (and not attached):
 [1] splines_3.5.0          lattice_0.20-35        colorspace_1.3-2      
 [4] htmltools_0.3.6        yaml_2.1.19            base64enc_0.1-3       
 [7] XML_3.98-1.11          survival_2.42-3        rlang_0.2.0           
[10] pillar_1.2.2           DBI_1.0.0              foreign_0.8-70        
[13] RColorBrewer_1.1-2     GenomeInfoDbData_1.1.0 plyr_1.8.4            
[16] stringr_1.3.1          zlibbioc_1.26.0        munsell_0.4.3         
[19] gtable_0.2.0           htmlwidgets_1.2        latticeExtra_0.6-28   
[22] knitr_1.20             htmlTable_1.11.2       Rcpp_0.12.17          
[25] acepack_1.4.1          xtable_1.8-2           scales_0.5.0          
[28] backports_1.1.2        checkmate_1.8.5        Hmisc_4.1-1           
[31] XVector_0.20.0         gridExtra_2.3          digest_0.6.15         
[34] stringi_1.2.2          grid_3.5.0             tools_3.5.0           
[37] bitops_1.0-6           magrittr_1.5           lazyeval_0.2.1        
[40] RCurl_1.95-4.10        tibble_1.4.2           Formula_1.2-3         
[43] cluster_2.0.7-1        Matrix_1.2-14          data.table_1.11.2     
[46] rstudioapi_0.7         rpart_4.1-13           nnet_7.3-12           
[49] compiler_3.5.0        
ADD COMMENTlink modified 27 days ago by Michael Love18k • written 28 days ago by CandiceChuDVM30
2
gravatar for Michael Love
27 days ago by
Michael Love18k
United States
Michael Love18k wrote:

How about at this stage:

"Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes"

Instead try: no

ADD COMMENTlink modified 27 days ago • written 27 days ago by Michael Love18k

Thanks! It worked! Here is what happened when I replied no

trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/bit_1.1-12.tgz'

Content type 'application/x-gzip' length 243803 bytes (238 KB)

==================================================

downloaded 238 KB

The downloaded binary packages are in

/var/folders/x7/cl6c9fjs0mq8k2lnrw7ls6q40000gn/T//RtmpLbCPrO/downloaded_packages

Old packages: 'bit', 'RcppArmadillo'

Update all/some/none? [a/s/n]: 

I then replied n, and it worked!

 

ADD REPLYlink modified 27 days ago • written 27 days ago by CandiceChuDVM30

Can't install DESeq2 have tried what you recommended but still can't install it the error message ...

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment

---- after trying to reinstall the missing packages another ERROR messages

> 
Warning in install.packages :
  packages ‘IRanges’, ‘GenomicRanges’, ‘GenomeInfoDb’, ‘SummarizedExperiment’ are not available (for R version 3.3.2)
Error in loadNamespace(name) : there is no package called ‘yaml’
Error in loadNamespace(name) : there is no package called ‘yaml’
--- Downloaded another R version but still 
Error: package or namespace load failed for ‘DESeq2

ANY IDEA please, thanks

ADD REPLYlink written 26 days ago by t.lem0
> library(DESeq2)

Error: package or namespace load failed for ‘DESeq2’

I appreciate your recommendation

ADD REPLYlink written 26 days ago by t.lem0

Because you are using an older version of R, I'd guess that you have some kind of mixed package version problem. Can you run:

library(BiocInstaller)
biocValid()
ADD REPLYlink written 26 days ago by Michael Love18k

It works thank you very much, indeed

ADD REPLYlink written 26 days ago by t.lem0
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