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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GOexpress_1.39.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.39.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GOexpress’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'getBM(attributes = microarray.header, ': unused argument (curl = curlHandle) 
  Note: possible error in 'getBM(attributes = "ensembl_gene_id", ': unused argument (curl = curl) 
See ‘/home/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GO_analyse: no visible binding for global variable ‘microarray2dataset’
GO_analyse: no visible binding for global variable ‘prefix2dataset’
mart_from_ensembl: no visible binding for global variable
  ‘prefix2dataset’
microarray2dataset.build: possible error in getBM(attributes =
  microarray.header, mart = mart.loop, curl = curlHandle): unused
  argument (curl = curlHandle)
sampleEnsemblGeneId: possible error in getBM(attributes =
  "ensembl_gene_id", mart = mart.loop, curl = curl): unused argument
  (curl = curl)
Undefined global functions or variables:
  microarray2dataset prefix2dataset
* checking Rd files ... NOTE
checkRd: (-1) AlvMac_GOgenes.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_GOgenes.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allGO.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allGO.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allGO.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allgenes.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allgenes.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allgenes.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hist_scores.Rd:11: Lost braces; missing escapes or markup?
    11 | variable of the {GO_analyse()} function.
       |                 ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GOexpress
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GOexpress’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'getBM(attributes = microarray.header, ': unused argument (curl = curlHandle) 
Note: possible error in 'getBM(attributes = "ensembl_gene_id", ': unused argument (curl = curl) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOexpress)