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### Running command:
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### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ChimpHumanBrainData.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ChimpHumanBrainData_1.39.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/ChimpHumanBrainData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ChimpHumanBrainData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChimpHumanBrainData’ version ‘1.39.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChimpHumanBrainData’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 64.7Mb
sub-directories of 1Mb or more:
extdata 64.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
MIT
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘DiffExpressVignette.Snw’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘DiffExpressVignette.Snw’
...
The downloaded source packages are in
‘/tmp/RtmpnWEqpj/downloaded_packages’
When sourcing ‘DiffExpressVignette.R’:
Error: Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Execution halted
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘DiffExpressVignette.Snw’ using Sweave
Loading required package: affy
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval,
evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: qvalue
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: hexbin
Loading required package: statmod
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’
trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.62.2.tar.gz'
Content type 'application/x-gzip' length 4359178 bytes (4.2 MB)
==================================================
downloaded 4.2 MB
trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/Rtmp4QGUYo/RLIBS_1489ab26e30f79/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/Rtmp4QGUYo/RLIBS_1489ab26e30f79/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/Rtmp4QGUYo/RLIBS_1489ab26e30f79/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(), :
installation of package ‘hgu95av2cdf’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpizfSvk/downloaded_packages’
Error: processing vignette 'DiffExpressVignette.Snw' failed with diagnostics:
chunk 6
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
--- failed re-building ‘DiffExpressVignette.Snw’
SUMMARY: processing the following file failed:
‘DiffExpressVignette.Snw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-data-experiment/meat/ChimpHumanBrainData.Rcheck/00check.log’
for details.