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Question: failure to install Homo.sapiens
0
gravatar for david.cherba
2.6 years ago by
david.cherba0 wrote:

trying to update package Homo.sapiens on a windows 7 64 bit R 3.2 and keep failing with 

It appears that not package that is xxxx.tar.gz will install correctly. 

Any ideas how to fix this.  I have tried manually unzip, untar and placing in the correct directory but it then indicates that the package was not installed correctly.. 

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2 (2015-08-14).
Installing package(s) ‘Homo.sapiens’
also installing the dependencies ‘GO.db’, ‘org.Hs.eg.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

installing the source packages ‘GO.db’, ‘org.Hs.eg.db’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘Homo.sapiens’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/GO.db_3.2.2.tar.gz'
Content type 'application/x-gzip' length 31248918 bytes (29.8 MB)
downloaded 29.8 MB

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Hs.eg.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 68856557 bytes (65.7 MB)
downloaded 65.7 MB

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz'
Content type 'application/x-gzip' length 18669702 bytes (17.8 MB)
downloaded 17.8 MB

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz'
Content type 'application/x-gzip' length 1617 bytes
downloaded 1617 bytes

'\\vaifile01\userdata\david.cherba\my documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'AnnotationDbi' was built under R version 3.2.3
Warning: package 'IRanges' was built under R version 3.2.3
Warning: package 'S4Vectors' was built under R version 3.2.3
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'GO.db'
Error: loading failed
Execution halted
*** arch - x64
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'GO.db'
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/GO.db'
* restoring previous '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/GO.db'
'\\vaifile01\userdata\david.cherba\my documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'AnnotationDbi' was built under R version 3.2.3
Warning: package 'IRanges' was built under R version 3.2.3
Warning: package 'S4Vectors' was built under R version 3.2.3
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'org.Hs.eg.db'
Error: loading failed
Execution halted
*** arch - x64
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'org.Hs.eg.db'
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/org.Hs.eg.db'
* restoring previous '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/org.Hs.eg.db'
'\\vaifile01\userdata\david.cherba\my documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'GenomicFeatures' was built under R version 3.2.3
Warning: package 'S4Vectors' was built under R version 3.2.3
Warning: package 'IRanges' was built under R version 3.2.3
Warning: package 'GenomeInfoDb' was built under R version 3.2.3
Warning: package 'GenomicRanges' was built under R version 3.2.3
Warning: package 'AnnotationDbi' was built under R version 3.2.3
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Error: loading failed
Execution halted
*** arch - x64
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
  there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/TxDb.Hsapiens.UCSC.hg19.knownGene'
* restoring previous '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/TxDb.Hsapiens.UCSC.hg19.knownGene'
'\\vaifile01\userdata\david.cherba\my documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'Homo.sapiens' ...
** R
** data
** preparing package for lazy loading
Warning: package 'AnnotationDbi' was built under R version 3.2.3
Warning: package 'IRanges' was built under R version 3.2.3
Warning: package 'S4Vectors' was built under R version 3.2.3
Warning: package 'OrganismDbi' was built under R version 3.2.3
Warning: package 'GenomicFeatures' was built under R version 3.2.3
Warning: package 'GenomeInfoDb' was built under R version 3.2.3
Warning: package 'GenomicRanges' was built under R version 3.2.3
Error : package 'GO.db' required by 'Homo.sapiens' could not be found
ERROR: lazy loading failed for package 'Homo.sapiens'
* removing '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/Homo.sapiens'
* restoring previous '\\vaifile01/userdata/David.Cherba/my documents/R/win-library/3.2/Homo.sapiens'

The downloaded source packages are in
        ‘C:\Users\david.cherba\AppData\Local\Temp\Rtmpa8QXOr\downloaded_packages’
Old packages: 'class', 'foreign', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet',
  'spatial'
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by david.cherba0
0
gravatar for James W. MacDonald
2.6 years ago by
United States
James W. MacDonald47k wrote:

This error:

'\\vaifile01\userdata\david.cherba\my documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.

Is coming directly from Windows, not R. You can google for example 'UNC paths are not supported', and maybe you will be able to come up with a fix. It sort of looks like you are trying to install packages on a server share? That might be problematic as well.

Do you get the same error if you try to install binary packages?

ADD COMMENTlink written 2.6 years ago by James W. MacDonald47k
0
gravatar for david.cherba
2.6 years ago by
david.cherba0 wrote:

I can install other packages without trouble.  It appears to be only those that are tar.gz. 

 

Dave

ADD COMMENTlink written 2.6 years ago by david.cherba0
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