===============================
R CMD BUILD
===============================
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* preparing ‘iNETgrate’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘iNETgrate/data/toyCleanedAml.rda’
‘iNETgrate/data/toyComputEloci.rda’
‘iNETgrate/data/toyEigengenes.rda’ ‘iNETgrate/data/toyRawAml.rda’
* building ‘iNETgrate_0.99.68.tar.gz’
===============================
BiocCheckGitClone('iNETgrate')
===============================
─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: iNETgrate
─ PackageVersion: 0.99.68
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2979/fe72943bf684e20658559f639a8ffda2b4ea0597/iNETgrate
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* 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...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2979/fe72943bf684e20658559f639a8ffda2b4ea0597/iNETgrate.Rcheck’
* using R version 4.3.0 RC (2023-04-18 r84287)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iNETgrate/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iNETgrate’ version ‘0.99.68’
* 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 ‘iNETgrate’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [29s/29s] OK
* checking whether the package can be loaded with stated dependencies ... [29s/29s] OK
* checking whether the package can be unloaded cleanly ... [22s/22s] OK
* checking whether the namespace can be loaded with stated dependencies ... [28s/28s] OK
* checking whether the namespace can be unloaded cleanly ... [37s/37s] OK
* checking loading without being on the library search path ... [29s/29s] 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 ... [137s/138s] OK
* checking Rd files ... [1s/1s] 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 ... ERROR
TIMEOUT: R CMD check exceeded 16 mins
===============================
BiocCheck('iNETgrate_0.99.68.tar.gz')
===============================
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 ...─ BiocCheckVersion: 1.37.0
─ BiocVersion: 3.18
─ Package: iNETgrate
─ PackageVersion: 0.99.68
─ sourceDir: /tmp/RtmpwTdtO2/filedd9ec93937b/iNETgrate
─ installDir: /tmp/RtmpwTdtO2/filedd9ec5acd88e5
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2979/fe72943bf684e20658559f639a8ffda2b4ea0597/iNETgrate.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 3.5.0 to 4.3.0.
* Checking package size...
[14s/14s] OK
* checking data for ASCII and uncompressed saves ...* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
toyCleanedAml.rda 1.9Mb 1.7Mb xz
toyComputEloci.rda 124Kb 105Kb xz
toyRawAml.rda 2.1Mb 1.8Mb xz
* checking files in ‘vignettes’ ... OK
* checking examples ...* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of iNETgrate...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 23 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 method overwritten by 'gplots':
method from
reorder.factor gdata
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 9% of man pages use at least one of these tags.
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 700 lines (11%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1058 lines
(16%) are not.
See https://contributions.bioconductor.org/r-code.html
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.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 9 NOTES
See the iNETgrate.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.