Question: BiocManager::install("hgu95av2.db") errror while Installin the hgu95avs.db package
0
gravatar for marwyelattar
3 months ago by
marwyelattar0 wrote:

When i try to install the hgu95av2.db" package using the line code:

 BiocManager::install("hgu95av2.db")  and also i tried
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GO.db", version = "3.8")

both commands give the same error

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'hgu95av2.db'
also installing the dependency ‘org.Hs.eg.db’

installing the source packages ‘org.Hs.eg.db’, ‘hgu95av2.db’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Hs.eg.db_3.7.0.tar.gz'
Content type 'application/x-gzip' length 77962833 bytes (74.4 MB)
downloaded 74.4 MB

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 502594 bytes (490 KB)
downloaded 490 KB

* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
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 'org.Hs.eg.db'
* removing 'C:/Users/Marwy/Documents/R/win-library/3.5/org.Hs.eg.db'
In R CMD INSTALL
ERROR: dependency 'org.Hs.eg.db' is not available for package 'hgu95av2.db'
* removing 'C:/Users/Marwy/Documents/R/win-library/3.5/hgu95av2.db'
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\Marwy\AppData\Local\Temp\RtmpC2ysug\downloaded_packages’


Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘org.Hs.eg.db’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘hgu95av2.db’ had non-zero exit status

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] strucchange_1.5-1   sandwich_2.5-0      zoo_1.8-4           modeltools_0.2-22   mvtnorm_1.0-10      affy_1.60.0        
[7] Biobase_2.42.0      BiocGenerics_0.28.0 limma_3.38.3       

loaded via a namespace (and not attached):
 [1] lattice_0.20-38       zlibbioc_1.28.0       affyio_1.52.0         rpart_4.1-13          preprocessCore_1.44.0
 [6] splines_3.5.2         tools_3.5.2           yaml_2.2.0            compiler_3.5.2        BiocManager_1.30.4   

Thanks

hgu95av2.db • 80 views
ADD COMMENTlink modified 3 months ago by James W. MacDonald50k • written 3 months ago by marwyelattar0
Answer: BiocManager::install("hgu95av2.db") errror while Installin the hgu95avs.db packa
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald50k wrote:

Try

BiocManager::install(c("Rcpp","AnnotationDbi","org.Hs.eg.db","hgu95av2.db"))

and let us know if that solves it.

ADD COMMENTlink written 3 months ago by James W. MacDonald50k
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