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Question: Unable to load package 'hgu95acdf' after upgrading to R 3.4.0
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gravatar for sue.wilson
13 months ago by
sue.wilson0
sue.wilson0 wrote:

I am using macOS 10.12.4 The package 'hgu95acdf' works with R 3.3.3,
but having just upgraded to R 3.4.0 now cannot load 'hgu95acdf'. Here is what I get:

> biocLite("hgu95acdf")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘hgu95acdf’
installing the source package ‘hgu95acdf’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331364 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘hgu95acdf’ ...
** R
** data
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘DBI’
ERROR: lazy loading failed for package ‘hgu95acdf’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/hgu95acdf’

The downloaded source packages are in
    ‘/private/var/folders/nj/4z75sb008xjfk40059bq1g0r0000gp/T/Rtmpcxmgk5/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘hgu95acdf’ had non-zero exit status

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] multtest_2.32.0      BiocInstaller_1.26.0 affy_1.54.0          Biobase_2.36.0       BiocGenerics_0.22.0 

loaded via a namespace (and not attached):
 [1] lattice_0.20-35       MASS_7.3-47           grid_3.4.0            stats4_3.4.0          zlibbioc_1.22.0      
 [6] affyio_1.46.0         Matrix_1.2-10         preprocessCore_1.38.0 splines_3.4.0         tools_3.4.0          
[11] survival_2.41-3       compiler_3.4.0     
ADD COMMENTlink modified 13 months ago • written 13 months ago by sue.wilson0

I had a similar problem when updating. I am not sure the solution that worked but note that biocLite search for Bioconductor version 3.4 instead of 3.5. I removed biocLite/BiocInstaller from all the paths from the .libPaths() and try using the online one.

ADD REPLYlink written 13 months ago by Lluís R330

@Lluis you can see from the original post that Bioconductor 3.5 / BiocInstaller 1.26.0 is being used. Also the path https://bioconductor.org/packages/3.5/... means that the Bioconductor 3.5 repository is being used. Lluis, your problem likely arose from trying to use the same .libPaths() between your previous version of R and your current version of R; it is best practice, even if painful, to 'start again', e.g., by manipulating .libPaths() (through environment variables or .Rprofile or .Renviron) so that you install all non-base R packages in a library that is unique to the version of Bioconductor in use.

ADD REPLYlink written 13 months ago by Martin Morgan ♦♦ 21k

Oh, I confused the removing with the installing path. Sorry.

I agree, I made that for another computer, but in my personal computer I realized too late :(

ADD REPLYlink written 13 months ago by Lluís R330
0
gravatar for Martin Morgan
13 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

The short solution is to install the missing dependency 'by hand'

biocLite("DBI")

There is somewhere a bug in the logic (I think of install.packages()), and it would be helpful if before installing DBI you tried first

install.packages("hgu95cdf", repos=BiocInstaller::biocinstallRepos())

and report whether that fails or succeeds, and to confirm that there really is no DBI package in your installed packages

"DBI" %in% rownames(installed.packages())

Reporting

.libPaths()

might also be useful

ADD COMMENTlink modified 13 months ago • written 13 months ago by Martin Morgan ♦♦ 21k

Here is what happened:

> install.packages("hgu95cdf", repos=BiocInstaller::biocinstallRepos())
Warning in install.packages :
  package ‘hgu95cdf’ is not available (for R version 3.4.0)
Warning in install.packages :
  cannot open URL 'https://bioconductor.org/packages/3.5/data/annotation/bin/macosx/el-capitan/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open URL 'https://bioconductor.org/packages/3.5/data/experiment/bin/macosx/el-capitan/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open URL 'https://cran.csiro.au/bin/macosx/el-capitan/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'
> biocLite("DBI")
Error in biocLite("DBI") : could not find function "biocLite"
> "DBI" %in% rownames(installed.packages())
[1] FALSE
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"

ADD REPLYlink written 13 months ago by sue.wilson0

Focusing on the task at hand, the biocLite() function is in the BiocInstaller package, so

BiocInstaller::biocLite("DBI")

or alternatively

source("https://bioconductor.org/biocLite.R")
biocLite("DBI")
ADD REPLYlink written 13 months ago by Martin Morgan ♦♦ 21k
0
gravatar for sue.wilson
13 months ago by
sue.wilson0
sue.wilson0 wrote:

I know the package is there, but still unable to install it - get the same error message as before.

ADD COMMENTlink written 13 months ago by sue.wilson0

It's not clear from your description what you mean.

ADD REPLYlink written 13 months ago by Martin Morgan ♦♦ 21k
0
gravatar for sue.wilson
13 months ago by
sue.wilson0
sue.wilson0 wrote:

Here is the latest session

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("DBI")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘DBI’
trying URL 'https://cran.csiro.au/bin/macosx/el-capitan/contrib/3.4/DBI_0.6-1.tgz'
Content type 'application/x-gzip' length 745824 bytes (728 KB)
==================================================
downloaded 728 KB


The downloaded binary packages are in
    /var/folders/nj/4z75sb008xjfk40059bq1g0r0000gp/T//RtmpWVWeCh/downloaded_packages
Old packages: 'preprocessCore'
Update all/some/none? [a/s/n]: 
a

[Then a whole lot of stuff giving total 43174, while limit is 5000]

The downloaded source packages are in
    ‘/private/var/folders/nj/4z75sb008xjfk40059bq1g0r0000gp/T/RtmpWVWeCh/downloaded_packages’
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("hgu95acdf")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘hgu95acdf’
installing the source package ‘hgu95acdf’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331364 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘hgu95acdf’ ...
** R
** data
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘RSQLite’
ERROR: lazy loading failed for package ‘hgu95acdf’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/hgu95acdf’

The downloaded source packages are in
    ‘/private/var/folders/nj/4z75sb008xjfk40059bq1g0r0000gp/T/RtmpWVWeCh/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘hgu95acdf’ had non-zero exit status

ADD COMMENTlink written 13 months ago by sue.wilson0

Again I don't know what the specific problem is that makes automatic package dependencies fail, but notice that the message you received earlier

** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘DBI’

Is the same sort of message that you are receiving now, but for a different package

** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘RSQLite’

Thus take the same solution -- try to install RSQLite

source("https://bioconductor.org/biocLite.R")
biocLite("RSQLite")

 

ADD REPLYlink written 13 months ago by Martin Morgan ♦♦ 21k
0
gravatar for sue.wilson
13 months ago by
sue.wilson0
sue.wilson0 wrote:

Many! thanks - this worked :-)
Your assistance is much appreciated.

ADD COMMENTlink written 13 months ago by sue.wilson0
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