Question: Problem in installing maEndToEnd package
0
gravatar for Jack
10 weeks ago by
Jack0
Jack0 wrote:

Dear Bioconductor admin,

I am working on data analysis for microarray data, but I could not install into my R studio,

Could you please help to solve my issue that How to install "maEndToEnd" into R studio in my Macbook?

Thank you very much

Here is the problem report from my screen:

> library(devtools)
> library(remotes)
> remotes::install_github("b-klaus/maEndToEnd", ref="master")
Downloading GitHub repo b-klaus/maEndToEnd@master
Skipping 42 packages ahead of CRAN: Biobase, oligoClasses, ArrayExpress, oligo, arrayQualityMetrics, limma, topGO, ReactomePA, clusterProfiler, geneplotter, genefilter, Rgraphviz, BiocGenerics, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, affyio, S4Vectors, AnnotationDbi, affxparser, preprocessCore, zlibbioc, affy, affyPLM, beadarray, vsn, graph, DOSE, enrichplot, graphite, GOSemSim, qvalue, annotate, GenomeInfoDb, XVector, DelayedArray, BiocParallel, gcrma, BeadDataPackR, illuminaio, fgsea
✔  checking for file ‘/private/var/folders/cy/rq7bxr0d7zx2vdh77jwng_4h0000gn/T/RtmpnI7Ct0/remotes19294101919d/b-klaus-maEndToEnd-2e5cae5/DESCRIPTION’ (411ms)
─  preparing ‘maEndToEnd’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘maEndToEnd_1.99.6.tar.gz’

* installing *source* package ‘maEndToEnd’ ...
** using staged installation
** inst
** help
No man pages found in package  ‘maEndToEnd’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘arrayQualityMetrics’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so, 6): Library not loaded: /opt/X11/lib/libcairo.2.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdtools/libs/gdtools.so
  Reason: image not found
Error : package ‘arrayQualityMetrics’ could not be loaded
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/maEndToEnd’
Error: Failed to install 'maEndToEnd' from GitHub:
  (converted from warning) installation of package ‘/var/folders/cy/rq7bxr0d7zx2vdh77jwng_4h0000gn/T//RtmpnI7Ct0/file19294dfefbc2/maEndToEnd_1.99.6.tar.gz’ had non-zero exit status
microarray maendtoend • 230 views
ADD COMMENTlink modified 16 days ago • written 10 weeks ago by Jack0

Could you try installing from Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# If you want the development versions of packages: 
BiocManager::install(version='devel')

BiocManager::install("maEndToEnd")

You could also check the installation of packages to make sure dependencies are up to date:

BiocManager::valid()
ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by shepherl ♦♦ 1.6k

I did try that method with many many times but it still showed the same problem, Could you please try with your Mac? I think this package has serious problem in installing

Thanks a lot

ADD REPLYlink written 10 weeks ago by Jack0

it still show

  • installing source package ‘maEndToEnd’ ... * using staged installation * inst * help No man pages found in package ‘maEndToEnd’ ** installing help indices * building package indices * installing vignettes ** testing if installed package can be loaded from temporary location
ADD REPLYlink written 10 weeks ago by Jack0
Answer: C: Problem in installing maEndToEnd package
1
gravatar for shepherl
10 weeks ago by
shepherl ♦♦ 1.6k
United States
shepherl ♦♦ 1.6k wrote:

The ERROR messages above are actually coming from arrayQualityMetrics package not being able to install. It looks like it actually has to do with system dependencies.

From some other packages that were having similar issues the suggestion is to reinstall XQuartz at https://www.xquartz.org/ and possibly a reinstall of cairo. (references: https://github.com/thomasp85/gganimate/issues/95 and https://github.com/davidgohel/gdtools/issues/43#issuecomment-375056815)

Could you please do a system reinstall of XQuartz and try installing in R arrayQualityMetrics. BiocManager::install("arrayQualityMetrics") and if those are successful then try maEndToEnd again.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by shepherl ♦♦ 1.6k

Awesome,

Thank you very much Shepherl,

It works perfectly now,

ADD REPLYlink written 10 weeks ago by Jack0

Dear Admin,

Last time, I had a problem with MacOS when I tried to install maEndToEnd into R, and it had been solved,

But I now have the same problem when running on Windows system,

Here are the errors showing

:
package ‘curl’ successfully unpacked and MD5 sums checked
Error: Failed to install 'maEndToEnd' from GitHub:
  (converted from warning) cannot remove prior installation of package ‘curl’
In addition: Warning messages:
1: In untar2(tarfile, files, list, exdir) :
  skipping pax global extended headers
2: In untar2(tarfile, files, list, exdir) :
  skipping pax global extended headers
> suppressPackageStartupMessages({library("maEndToEnd")})
 Error in library("maEndToEnd") : there is no package called ‘maEndToEnd’

Could you please help me in this case? Thank you very much Best regards Truong

ADD REPLYlink written 23 days ago by Jack0

Can you please show the results of

.libPaths()
sessionInfo()

From the sound of the ERROR, you might have multiple installations paths, one of which is not writable and cannot update the package curl.

ADD REPLYlink written 23 days ago by shepherl ♦♦ 1.6k

It also could be that another application was using curl when you tried to update. You could also do repeated calls to remove.packages("curl") until R says the library cannot be found. Then do BiocManager::install("curl") and BiocManager::install("maEndToEnd"). This should remove curl, reinstall curl, and install maEndToEnd.

ADD REPLYlink written 23 days ago by shepherl ♦♦ 1.6k

I did try this way as your instruction, but it still did not work,

Many Thanks

ADD REPLYlink written 21 days ago by Jack0

It showed:

The downloaded source packages are in
    ‘C:\Users\linht\AppData\Local\Temp\RtmpWGu4IU\downloaded_packages’
installation path not writeable, unable to update packages: boot, foreign, mgcv,
  nlme
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘pd.hugene.1.0.st.v1’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘maEndToEnd’ had non-zero exit status
Error in library("maEndToEnd") : there is no package called ‘maEndToEnd’
ADD REPLYlink written 21 days ago by Jack0
The downloaded source packages are in
    ‘C:\Users\linht\AppData\Local\Temp\RtmpWGu4IU\downloaded_packages’
installation path not writeable, unable to update packages: boot, foreign, mgcv,
  nlme
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘pd.hugene.1.0.st.v1’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘maEndToEnd’ had non-zero exit status
Error in library("maEndToEnd") : there is no package called ‘maEndToEnd’
ADD REPLYlink written 17 days ago by Jack0

Can you try just installing pd.hugene.1.0.st.v1 and display the full output ERROR

BiocManager::install('pd.hugene.1.0.st.v1')
ADD REPLYlink written 17 days ago by shepherl ♦♦ 1.6k

Thank you very much Shepherl, and Here is the output results:

> BiocManager::install('pd.hugene.1.0.st.v1')
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'pd.hugene.1.0.st.v1'
installing the source package ‘pd.hugene.1.0.st.v1’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz'
Content type 'application/x-gzip' length 82353509 bytes (78.5 MB)
downloaded 78.5 MB

* installing *source* package 'pd.hugene.1.0.st.v1' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'RSQLite' was built under R version 3.5.3
Error: package or namespace load failed for 'RSQLite' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'digest'
Error : package 'RSQLite' could not be loaded
ERROR: lazy loading failed for package 'pd.hugene.1.0.st.v1'
* removing 'C:/Users/acer/Documents/R/win-library/3.5/pd.hugene.1.0.st.v1'
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages’
installation path not writeable, unable to update packages: boot, class, cluster,
  codetools, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, Rserve, survival
Update old packages: 'DescTools', 'rvcheck'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
        binary source needs_compilation
rvcheck  0.1.3  0.1.5             FALSE

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/DescTools_0.99.29.zip'
Content type 'application/zip' length 5346554 bytes (5.1 MB)
downloaded 5.1 MB

package ‘DescTools’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages
installing the source package ‘rvcheck’

trying URL 'https://cran.rstudio.com/src/contrib/rvcheck_0.1.5.tar.gz'
Content type 'application/x-gzip' length 5488 bytes
downloaded 5488 bytes

* installing *source* package 'rvcheck' ...
** package 'rvcheck' successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rvcheck'
    finding HTML links ... done
    check_bioc                              html  
    check_cran                              html  
    check_github                            html  
    check_gitlab                            html  
    check_r                                 html  
    get_aes_var                             html  
    get_fun_from_pkg                        html  
    o                                       html  
    read.cb                                 html  
    update_all                              html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (rvcheck)
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘pd.hugene.1.0.st.v1’ had non-zero exit status
ADD REPLYlink written 17 days ago by Jack0

And if you did

BiocManager::install('digest')

To install the missing digest package? And then try installing pd.hugene.1.0.st.v1 again?

ADD REPLYlink written 17 days ago by shepherl ♦♦ 1.6k

after install ('digest')

> BiocManager::install('digest')
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'digest'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/digest_0.6.21.zip'
Content type 'application/zip' length 237331 bytes (231 KB)
downloaded 231 KB

package ‘digest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages
installation path not writeable, unable to update packages: boot, class, cluster,
  codetools, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, Rserve, survival
> BiocManager::install('pd.hugene.1.0.st.v1')
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'pd.hugene.1.0.st.v1'
installing the source package ‘pd.hugene.1.0.st.v1’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz'
Content type 'application/x-gzip' length 82353509 bytes (78.5 MB)
downloaded 78.5 MB

* installing *source* package 'pd.hugene.1.0.st.v1' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'RSQLite' was built under R version 3.5.3
Warning: package 'DBI' was built under R version 3.5.3
** help
*** installing help indices
  converting help for package 'pd.hugene.1.0.st.v1'
    finding HTML links ... done
    pkg                                     html  
    probeSequences                          html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'RSQLite' was built under R version 3.5.3
Warning: package 'DBI' was built under R version 3.5.3
*** arch - x64
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'RSQLite' was built under R version 3.5.3
Warning: package 'DBI' was built under R version 3.5.3
* DONE (pd.hugene.1.0.st.v1)
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages’
installation path not writeable, unable to update packages: boot, class, cluster,
  codetools, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, Rserve, survival
ADD REPLYlink written 17 days ago by Jack0

Okay those two looks successful and now if you try maEndToEnd again?

ADD REPLYlink written 17 days ago by shepherl ♦♦ 1.6k

Here is again running for :

> BiocManager::install('pd.hugene.1.0.st.v1')
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'pd.hugene.1.0.st.v1'
installing the source package ‘pd.hugene.1.0.st.v1’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz'
Content type 'application/x-gzip' length 82353509 bytes (78.5 MB)
downloaded 78.5 MB

* installing *source* package 'pd.hugene.1.0.st.v1' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'RSQLite' was built under R version 3.5.3
Warning: package 'DBI' was built under R version 3.5.3
** help
*** installing help indices
  converting help for package 'pd.hugene.1.0.st.v1'
    finding HTML links ... done
    pkg                                     html  
    probeSequences                          html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'RSQLite' was built under R version 3.5.3
Warning: package 'DBI' was built under R version 3.5.3
*** arch - x64
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'RSQLite' was built under R version 3.5.3
Warning: package 'DBI' was built under R version 3.5.3
* DONE (pd.hugene.1.0.st.v1)
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages’
installation path not writeable, unable to update packages: boot, class, cluster,
  codetools, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, Rserve, survival
ADD REPLYlink modified 16 days ago • written 17 days ago by Jack0

No problem. It looks like pd.hugene.1.0.st.v1 installed correctly which was ERROR when you originally tried maEndToEnd. Can you see if BiocManager::install('maEndToEnd') now will install?

ADD REPLYlink written 17 days ago by shepherl ♦♦ 1.6k

I run again:

BiocManager::install("maEndToEnd") Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02) Installing package(s) 'maEndToEnd' also installing the dependency ‘hugene10sttranscriptcluster.db’

installing the source packages ‘hugene10sttranscriptcluster.db’, ‘maEndToEnd’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10sttranscriptcluster.db_8.7.0.tar.gz' Content type 'application/x-gzip' length 3879250 bytes (3.7 MB) downloaded 3.7 MB

trying URL 'https://bioconductor.org/packages/3.8/workflows/src/contrib/maEndToEnd_2.0.0.tar.gz' Content type 'application/x-gzip' length 5730252 bytes (5.5 MB) downloaded 5.5 MB

  • installing source package 'hugene10sttranscriptcluster.db' ... * R * inst * byte-compile and prepare package for lazy loading * help * installing help indices converting help for package 'hugene10sttranscriptcluster.db' finding HTML links ... done hugene10sttranscriptclusterACCNUM html
    hugene10sttranscriptclusterALIAS2PROBE html
    hugene10sttranscriptclusterBASE html
    hugene10sttranscriptclusterCHR html
    hugene10sttranscriptclusterCHRLENGTHS html
    hugene10sttranscriptclusterCHRLOC html
    hugene10sttranscriptclusterENSEMBL html
    hugene10sttranscriptclusterENTREZID html
    hugene10sttranscriptclusterENZYME html
    hugene10sttranscriptclusterGENENAME html
    hugene10sttranscriptclusterGO html
    hugene10sttranscriptclusterMAP html
    hugene10sttranscriptclusterMAPCOUNTS html
    hugene10sttranscriptclusterOMIM html
    hugene10sttranscriptclusterORGANISM html
    hugene10sttranscriptclusterPATH html
    hugene10sttranscriptclusterPFAM html
    hugene10sttranscriptclusterPMID html
    hugene10sttranscriptclusterPROSITE html
    hugene10sttranscriptclusterREFSEQ html
    hugene10sttranscriptclusterSYMBOL html
    hugene10sttranscriptclusterUNIGENE html
    hugene10sttranscriptclusterUNIPROT html
    hugene10sttranscriptcluster_dbconn html
    * building package indices * testing if installed package can be loaded
    arch - i386 ** arch - x64
  • DONE (hugene10sttranscriptcluster.db) In R CMD INSTALL
  • installing source package 'maEndToEnd' ... * inst * help No man pages found in package 'maEndToEnd' * installing help indices * building package indices * installing vignettes * testing if installed package can be loaded * arch - i386 Warning: package 'Biostrings' was built under R version 3.5.2 Warning: package 'RSQLite' was built under R version 3.5.3 Warning: package 'DBI' was built under R version 3.5.3 Error: package or namespace load failed for 'arrayQualityMetrics' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'gridSVG' Error : package 'arrayQualityMetrics' could not be loaded Error: loading failed Execution halted ** arch - x64 Warning: package 'Biostrings' was built under R version 3.5.2 Warning: package 'RSQLite' was built under R version 3.5.3 Warning: package 'DBI' was built under R version 3.5.3 Error: package or namespace load failed for 'arrayQualityMetrics' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'gridSVG' Error : package 'arrayQualityMetrics' could not be loaded Error: loading failed Execution halted ERROR: loading failed for 'i386', 'x64'
  • removing 'C:/Users/acer/Documents/R/win-library/3.5/maEndToEnd' In R CMD INSTALL

The downloaded source packages are in ‘C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages’ installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign, lattice, MASS, Matrix, mgcv, nlme, rpart, Rserve, survival Warning message: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘maEndToEnd’ had non-zero exit status

library(maEndToEnd) Error in library(maEndToEnd) : there is no package called ‘maEndToEnd’

ADD REPLYlink written 17 days ago by Jack0

So generally when the ERROR says there is no package called '<somepackage> it means that that package hasn't been installed with BiocManager::install and you should try and install that package. So in this case: BiocManager::install('gridSVG') . I'm surprised a lot of these dependencies aren't automatically detected and installed. Can you try running BiocManager::install('maEndToEnd', dependencies=c("Depends", "Imports", "LinkingTo", "Suggests","Enhances") If the dependencies were stated correctly I think that might start picking up the nested dependencies better.

ADD REPLYlink written 17 days ago by shepherl ♦♦ 1.6k

I followed your guidance and re-run within 3 hours with a lot Gb of storage, but it still show:

Rd warning: C:/Users/acer/AppData/Local/Temp/RtmpUJcmpM/R.INSTALLdc012e67d0c/BSgenome.Hsapiens.UCSC.hg38.masked/man/package.Rd:41: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/acer/AppData/Local/Temp/RtmpUJcmpM/R.INSTALLdc012e67d0c/BSgenome.Hsapiens.UCSC.hg38.masked/man/package.Rd:44: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'rtracklayer' was built under R version 3.5.2
*** arch - x64
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
Warning: package 'Biostrings' was built under R version 3.5.2
Warning: package 'rtracklayer' was built under R version 3.5.2
* DONE (BSgenome.Hsapiens.UCSC.hg38.masked)
In R CMD INSTALL
* installing *source* package 'Rattus.norvegicus' ...
** R
** data
** byte-compile and prepare package for lazy loading
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
** help
*** installing help indices
  converting help for package 'Rattus.norvegicus'
    finding HTML links ... done
    Rattus.norvegicus                       html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
*** arch - x64
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
* DONE (Rattus.norvegicus)
In R CMD INSTALL
* installing *source* package 'Homo.sapiens' ...
** R
** data
** byte-compile and prepare package for lazy loading
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
** help
*** installing help indices
  converting help for package 'Homo.sapiens'
    finding HTML links ... done
    Homo.sapiens                            html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
*** arch - x64
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
* DONE (Homo.sapiens)
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages’
installation path not writeable, unable to update packages: boot, class, cluster,
  codetools, foreign, lattice, MASS, Matrix, mgcv, rpart, Rserve, survival
Update old packages: 'EpiModel', 'nlme'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
          binary  source needs_compilation
EpiModel   1.7.2   1.7.3              TRUE
nlme     3.1-137 3.1-141              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/EpiModel_1.7.2.zip'
Content type 'application/zip' length 959898 bytes (937 KB)
downloaded 937 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/nlme_3.1-137.zip'
Content type 'application/zip' length 2346045 bytes (2.2 MB)
downloaded 2.2 MB

package ‘EpiModel’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\acer\AppData\Local\Temp\Rtmpek0PPR\downloaded_packages
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘statnet’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘maEndToEnd’ had non-zero exit status
> 
> library(maEndToEnd)
Error in library(maEndToEnd) : there is no package called ‘maEndToEnd’
>
ADD REPLYlink written 17 days ago by Jack0
1

And if you do: BiocManager::install(c('statnet', 'maEndToEnd') ?

ADD REPLYlink written 16 days ago by shepherl ♦♦ 1.6k
1

Problem with using dependencies=c("Depends", "Imports", "LinkingTo", "Suggests","Enhances") is that it tends to install way to many packages, and many of them are actually never used/needed by the package that you're trying to install (in this case maEndToEnd). This is the case for statnet. It's not needed to get a fully functioning maEndToEnd workflow. If you look at what's installed on our build machines (e.g. https://bioconductor.org/checkResults/3.9/bioc-LATEST/malbec2-R-instpkgs.html or https://bioconductor.org/checkResults/3.9/bioc-LATEST/tokay2-R-instpkgs.html), you'll see that statnet is not installed there. This means that no Bioconductor package actually needs statnet.

The reason dependencies=c("Depends", "Imports", "LinkingTo", "Suggests","Enhances") tends to install way too many packages is because packages that are listed in the Suggests and Enhances field of all the dependencies, direct or indirect, also get installed, together with their own dependencies, including packages that they in turn list in their Suggests and Enhances field, and so on... So it's not too surprising that the whole process took 3h and many Gb of storage to complete.

One thing I noticed is that the OP is using BioC 3.8 & R 3.5.1, which is no longer supported. It might be easier to start with a fresh R 3.6 install and do install.packages("BiocManager"); BiocManager::install("maEndToEnd") from there. This will install the current version of Bioconductor (3.9).

ADD REPLYlink modified 16 days ago • written 16 days ago by Hervé Pagès ♦♦ 14k

Hello Shepherl and Herve Pages,

Many thanks for your kind supports,

May problems has been solved!

Best regards

ADD REPLYlink written 16 days ago by Jack0
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