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'