===============================
R CMD BUILD
===============================
* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* preparing ‘cogeqc’:
* 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 ‘cogeqc_0.99.1.tar.gz’
===============================
BiocCheckGitClone('cogeqc')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2559/2edfb822429acb42016c8d1e7e9203266c6acdbb/cogeqc.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* this is package ‘cogeqc’ version ‘0.99.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cogeqc’ can be installed ... [7s/7s] 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 R 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 use of S3 registration ... 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 ... [9s/9s] OK
* 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [12s/12s]
[13s/13s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
===============================
BiocCheck('cogeqc_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2559/2edfb822429acb42016c8d1e7e9203266c6acdbb/cogeqc_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpySBLVC/fileb1d44f43ab93/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1 to 4.2.0.
* 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...
* NOTE: Consider adding these automatically suggested biocViews:
NetworkInference, Network
See http://bioconductor.org/developers/how-to/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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of cogeqc...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
run_busco.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
4% of man pages use one of these cases.
Found in the following files:
run_busco.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 39 lines (2%) are > 80 characters
long.
First 6 lines:
R/visualization.R:12 #' @param stats_list (optional) A list of data fra...
R/visualization.R:145 #' @param stats_list (optional) A list of data fr...
R/visualization.R:285 p <- ggplot2::ggplot(sizes, ggplot2::aes_...
R/visualization.R:296 p <- ggplot2::ggplot(sizes, ggplot2::aes_...
man/assess_synnet.Rd:5 \title{Assess synteny network based on clusterin...
man/plot_orthofinder_stats.Rd:17 \item{stats_list}{(optional) A list of...
* NOTE: Consider multiples of 4 spaces for line indents, 80
lines(3%) are not.
First 6 lines:
R/file_import.R:87 fragmented, mis...
R/file_import.R:94 "Complete_duplicate", "Fra...
R/file_import.R:157 row.names = 1)
R/file_import.R:160 "N_ssOGs", "N_genes_in_ssOGs"...
R/genome_assembly.R:62 mode = c("genome", "transc...
R/genome_assembly.R:63 lineage = NULL, auto_linea...
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir cogeqc_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘cogeqc’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (cogeqc)
===============================
R CMD BUILD
===============================
* checking for file ‘cogeqc/DESCRIPTION’ ... OK
* preparing ‘cogeqc’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette_01_assessing_genome_assembly.Rmd’ using rmarkdown
--- finished re-building ‘vignette_01_assessing_genome_assembly.Rmd’
--- re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’ using rmarkdown
Quitting from lines 219-220 (vignette_02_assessing_orthogroup_inference.Rmd)
Error: processing vignette 'vignette_02_assessing_orthogroup_inference.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘vignette_02_assessing_orthogroup_inference.Rmd’
--- re-building ‘vignette_03_assessing_synteny.Rmd’ using rmarkdown
Quitting from lines 100-101 (vignette_03_assessing_synteny.Rmd)
Error: processing vignette 'vignette_03_assessing_synteny.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘vignette_03_assessing_synteny.Rmd’
SUMMARY: processing the following files failed:
‘vignette_02_assessing_orthogroup_inference.Rmd’
‘vignette_03_assessing_synteny.Rmd’
Error: Vignette re-building failed.
Execution halted