===============================
R CMD BUILD
===============================
* checking for file omXplore/DESCRIPTION ... OK
* preparing omXplore:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a data/datalist file should be added
* building omXplore_0.99.2.tar.gz
===============================
BiocCheckGitClone('omXplore')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: omXplore
PackageVersion: 0.99.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3347/omXplore_20240404141847/omXplore
platform: unix
isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
omXplore.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
* WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint
or publication associated with this Bioconductor package.
BiocCheck results
1 ERRORS | 1 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3347/omXplore_20240404141847/omXplore.Rcheck
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file omXplore/DESCRIPTION ... OK
* checking extension type ... Package
* this is package omXplore version 0.99.2
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.github
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 omXplore can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking whether startup messages can be suppressed ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: Biobase
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [45s/45s] NOTE
Build_X_CC: no visible global function definition for metadata
Build_X_CC: no visible global function definition for metadata<-
Check_MSnSet_Consistency : <anonymous>: no visible global function
definition for experimentData
MAE_Compatibility_with_Prostar_1x : <anonymous>: no visible binding for
global variable .colData
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for experimentData
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for metadata
SE_Compatibility_with_Prostar_1.x: no visible global function
definition for metadata<-
Undefined global functions or variables:
.colData experimentData metadata metadata<-
Found the following assignments to the global environment:
File omXplore/R/modules.R:
assign(f_dest_name, eval(parse(text = f_fullname)), envir = globalenv())
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... ERROR
Warning: parse error in file 'lines':
5: unexpected ')'
310: ## Don't show:
311: if ()
^
** will not attempt to run examples
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [13s/13s]
[13s/13s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3347/omXplore_20240404141847/omXplore.Rcheck/00check.log
for details.
===============================
BiocCheck('omXplore_0.99.2.tar.gz')
===============================
BiocCheckVersion: 1.39.27
BiocVersion: 3.19
Package: omXplore
PackageVersion: 0.99.2
sourceDir: /tmp/RtmpOU0Wqp/file3103c51e7a1295/omXplore
installDir: /tmp/RtmpOU0Wqp/file3103c53d1d6a92
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3347/omXplore_20240404141847/omXplore.BiocCheck
platform: unix
isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.3.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (15%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Error in parse(outfile, keep.source = TRUE) :
/tmp/RtmpOU0Wqp/file3103c57d748f2/parseFile.tmp:8:5: unexpected ')'
7: ## Don't show:
8: if ()
^
Calls: BiocCheck -> BiocCheckRun -> parseFiles -> parseFile -> parse
Execution halted