Entering edit mode
priyanka_jain
•
0
@priyanka_jain-23589
Last seen 5.5 years ago
Kindly solve the error. I am unable to install GO.db
> BiocManager::install("GO.db")
Bioconductor version 3.6 (BiocManager 1.30.10), R 3.4.0 (2017-04-21)
Installing package(s) 'BiocVersion', 'GO.db'
installing the source package ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/GO.db_3.5.0.tar.gz'
Content type 'application/x-gzip' length 31663705 bytes (30.2 MB)
downloaded 30.2 MB
* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'AnnotationDbi' was built under R version 3.4.2
Warning: package 'BiocGenerics' was built under R version 3.4.2
Warning: package 'Biobase' was built under R version 3.4.2
Warning: package 'IRanges' was built under R version 3.4.2
Warning: package 'S4Vectors' was built under R version 3.4.2
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'Rcpp'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'GO.db'
* removing 'E:/user/Documents/R/win-library/3.4/GO.db'
The downloaded source packages are in
‘C:\Users\user\AppData\Local\Temp\RtmpaExEvE\downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, cluster, codetools, KernSmooth,
lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial
Old packages: 'backports', 'bit', 'checkmate', 'data.table', 'digest', 'ellipsis', 'fansi', 'farver',
'glue', 'Hmisc', 'htmltools', 'isoband', 'jsonlite', 'markdown', 'matrixStats', 'mime', 'processx', 'ps',
'rlang', 'RSQLite', 'scales', 'stringi', 'survival', 'testthat', 'tibble', 'vctrs', 'WGCNA', 'yaml'
Update all/some/none? [a/s/n]:
a
Warning: dependency ‘latticeExtra’ is not available
also installing the dependencies ‘Rcpp’, ‘blob’, ‘lifecycle’, ‘GO.db’
There are binary versions available but the source versions are later:
binary source needs_compilation
Rcpp 1.0.1 1.0.4.6 TRUE
blob 1.1.1 1.2.1 FALSE
backports 1.1.4 1.1.7 TRUE
bit 1.1-14 1.1-15.2 TRUE
checkmate 1.9.1 2.0.0 TRUE
data.table 1.12.2 1.12.8 TRUE
digest 0.6.18 0.6.25 TRUE
ellipsis 0.1.0 0.3.1 TRUE
fansi 0.4.0 0.4.1 TRUE
farver 1.1.0 2.0.3 TRUE
glue 1.3.1 1.4.1 TRUE
Hmisc 4.2-0 4.4-0 TRUE
htmltools 0.3.6 0.4.0 TRUE
isoband 0.2.0 0.2.1 TRUE
jsonlite 1.6 1.6.1 TRUE
markdown 0.9 1.1 TRUE
matrixStats 0.54.0 0.56.0 TRUE
mime 0.6 0.9 TRUE
processx 3.3.0 3.4.2 TRUE
ps 1.3.0 1.3.3 TRUE
rlang 0.3.4 0.4.6 TRUE
RSQLite 2.1.1 2.2.0 TRUE
scales 1.0.0 1.1.1 TRUE
stringi 1.4.3 1.4.6 TRUE
survival 2.44-1.1 3.1-12 TRUE
testthat 2.1.1 2.3.2 TRUE
tibble 2.1.1 3.0.1 TRUE
vctrs 0.1.0 0.3.0 TRUE
WGCNA 1.67 1.69 TRUE
yaml 2.2.0 2.2.1 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/Rcpp_1.0.1.zip'
Content type 'application/zip' length 4376246 bytes (4.2 MB)
downloaded 4.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/backports_1.1.4.zip'
Content type 'application/zip' length 66361 bytes (64 KB)
downloaded 64 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/bit_1.1-14.zip'
Content type 'application/zip' length 246271 bytes (240 KB)
downloaded 240 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/checkmate_1.9.1.zip'
Content type 'application/zip' length 735324 bytes (718 KB)
downloaded 718 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/data.table_1.12.2.zip'
Content type 'application/zip' length 1926960 bytes (1.8 MB)
downloaded 1.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/digest_0.6.18.zip'
Content type 'application/zip' length 176442 bytes (172 KB)
downloaded 172 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/ellipsis_0.1.0.zip'
Content type 'application/zip' length 30847 bytes (30 KB)
downloaded 30 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/fansi_0.4.0.zip'
Content type 'application/zip' length 186895 bytes (182 KB)
downloaded 182 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/farver_1.1.0.zip'
Content type 'application/zip' length 709275 bytes (692 KB)
downloaded 692 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/glue_1.3.1.zip'
Content type 'application/zip' length 172415 bytes (168 KB)
downloaded 168 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/Hmisc_4.2-0.zip'
Content type 'application/zip' length 1859845 bytes (1.8 MB)
downloaded 1.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/htmltools_0.3.6.zip'
Content type 'application/zip' length 617917 bytes (603 KB)
downloaded 603 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/isoband_0.2.0.zip'
Content type 'application/zip' length 2880152 bytes (2.7 MB)
downloaded 2.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/jsonlite_1.6.zip'
Content type 'application/zip' length 1116765 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/markdown_0.9.zip'
Content type 'application/zip' length 169076 bytes (165 KB)
downloaded 165 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/matrixStats_0.54.0.zip'
Content type 'application/zip' length 1634162 bytes (1.6 MB)
downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/mime_0.6.zip'
Content type 'application/zip' length 38886 bytes (37 KB)
downloaded 37 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/processx_3.3.0.zip'
Content type 'application/zip' length 246452 bytes (240 KB)
downloaded 240 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/ps_1.3.0.zip'
Content type 'application/zip' length 258393 bytes (252 KB)
downloaded 252 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/rlang_0.3.4.zip'
Content type 'application/zip' length 1080437 bytes (1.0 MB)
downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/RSQLite_2.1.1.zip'
Content type 'application/zip' length 2097863 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/scales_1.0.0.zip'
Content type 'application/zip' length 940439 bytes (918 KB)
downloaded 918 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/stringi_1.4.3.zip'
Content type 'application/zip' length 15213155 bytes (14.5 MB)
downloaded 14.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/survival_2.44-1.1.zip'
Content type 'application/zip' length 5102245 bytes (4.9 MB)
downloaded 4.9 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/testthat_2.1.1.zip'
Content type 'application/zip' length 1243585 bytes (1.2 MB)
downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/tibble_2.1.1.zip'
Content type 'application/zip' length 238931 bytes (233 KB)
downloaded 233 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/vctrs_0.1.0.zip'
Content type 'application/zip' length 499748 bytes (488 KB)
downloaded 488 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/WGCNA_1.67.zip'
Content type 'application/zip' length 2605570 bytes (2.5 MB)
downloaded 2.5 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/yaml_2.2.0.zip'
Content type 'application/zip' length 200401 bytes (195 KB)
downloaded 195 KB
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Rcpp’
package ‘backports’ successfully unpacked and MD5 sums checked
package ‘bit’ successfully unpacked and MD5 sums checked
package ‘checkmate’ successfully unpacked and MD5 sums checked
package ‘data.table’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘ellipsis’ successfully unpacked and MD5 sums checked
package ‘fansi’ successfully unpacked and MD5 sums checked
package ‘farver’ successfully unpacked and MD5 sums checked
package ‘glue’ successfully unpacked and MD5 sums checked
package ‘Hmisc’ successfully unpacked and MD5 sums checked
package ‘htmltools’ successfully unpacked and MD5 sums checked
package ‘isoband’ successfully unpacked and MD5 sums checked
package ‘jsonlite’ successfully unpacked and MD5 sums checked
package ‘markdown’ successfully unpacked and MD5 sums checked
package ‘matrixStats’ successfully unpacked and MD5 sums checked
package ‘mime’ successfully unpacked and MD5 sums checked
package ‘processx’ successfully unpacked and MD5 sums checked
package ‘ps’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
package ‘scales’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘survival’ successfully unpacked and MD5 sums checked
package ‘testthat’ successfully unpacked and MD5 sums checked
package ‘tibble’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘WGCNA’ successfully unpacked and MD5 sums checked
package ‘yaml’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\user\AppData\Local\Temp\RtmpaExEvE\downloaded_packages
installing the source packages ‘blob’, ‘lifecycle’, ‘GO.db’
trying URL 'https://cran.rstudio.com/src/contrib/blob_1.2.1.tar.gz'
Content type 'application/x-gzip' length 10099 bytes
downloaded 10099 bytes
trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_0.2.0.tar.gz'
Content type 'application/x-gzip' length 164455 bytes (160 KB)
downloaded 160 KB
trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/GO.db_3.5.0.tar.gz'
Content type 'application/x-gzip' length 31663705 bytes (30.2 MB)
downloaded 30.2 MB
* installing *source* package 'blob' ...
** package 'blob' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'vctrs' 0.1.0 is being loaded, but >= 0.2.1 is required
ERROR: lazy loading failed for package 'blob'
* removing 'E:/user/Documents/R/win-library/3.4/blob'
* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 0.3.4 is being loaded, but >= 0.4.0 is required
ERROR: lazy loading failed for package 'lifecycle'
* removing 'E:/user/Documents/R/win-library/3.4/lifecycle'
* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'AnnotationDbi' was built under R version 3.4.2
Warning: package 'BiocGenerics' was built under R version 3.4.2
Warning: package 'Biobase' was built under R version 3.4.2
Warning: package 'IRanges' was built under R version 3.4.2
Warning: package 'S4Vectors' was built under R version 3.4.2
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'Rcpp'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'GO.db'
* removing 'E:/user/Documents/R/win-library/3.4/GO.db'
The downloaded source packages are in
‘C:\Users\user\AppData\Local\Temp\RtmpaExEvE\downloaded_packages’
Warning messages:
1: package ‘BiocVersion’ is not available (for R version 3.4.0)
2: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "E:\user\Documents\R\win-library\3.4" C:\Users\user\AppData\Local\Temp\RtmpaExEvE/downloaded_packages/GO.db_3.5.0.tar.gz' had status 1
3: In install.packages(...) :
installation of package ‘GO.db’ had non-zero exit status
4: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "E:\user\Documents\R\win-library\3.4" C:\Users\user\AppData\Local\Temp\RtmpaExEvE/downloaded_packages/blob_1.2.1.tar.gz' had status 1
5: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘blob’ had non-zero exit status
6: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "E:\user\Documents\R\win-library\3.4" C:\Users\user\AppData\Local\Temp\RtmpaExEvE/downloaded_packages/lifecycle_0.2.0.tar.gz' had status 1
7: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘lifecycle’ had non-zero exit status
8: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "E:\user\Documents\R\win-library\3.4" C:\Users\user\AppData\Local\Temp\RtmpaExEvE/downloaded_packages/GO.db_3.5.0.tar.gz' had status 1
9: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘GO.db’ had non-zero exit status
