===============================
R CMD BUILD
===============================
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* preparing ‘dreamlet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: dreamlet
* saving partial Rd database
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘dreamlet_0.99.8.tar.gz’
===============================
BiocCheckGitClone('dreamlet')
===============================
─ BiocCheckVersion: 1.35.16
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.8
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/09b88a9ef9600476fe5d7fd5456c256e919e26ca/dreamlet
─ 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/2955/09b88a9ef9600476fe5d7fd5456c256e919e26ca/dreamlet.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* 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 ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘0.99.8’
* 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 ‘dreamlet’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [37s/37s] OK
* checking Rd files ... [10s/10s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... [169s/170s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
zenith_gsa-methods 51.149 1.692 53.214
sortCols-method 10.314 0.080 10.399
fitVarPart 9.918 0.092 10.011
plotVarPart-methods 9.612 0.072 9.685
plotPercentBars-methods 9.335 0.023 9.359
run_mash 8.864 0.072 8.937
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [32s/43s]
[32s/44s] 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 ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2955/09b88a9ef9600476fe5d7fd5456c256e919e26ca/dreamlet.Rcheck/00check.log’
for details.
===============================
BiocCheck('dreamlet_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.35.16
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.8
─ sourceDir: /tmp/RtmpavkwGc/file272f794106ac0b/dreamlet
─ installDir: /tmp/RtmpavkwGc/file272f79ad919f7
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/09b88a9ef9600476fe5d7fd5456c256e919e26ca/dreamlet.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 4.2.0 to 4.3.0.
* 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:
Microarray
Search 'biocViews' at https://contributions.bioconductor.org
* 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: Evaluate more vignette chunks.
61 code chunks / 80 total = 76% percent unevaluated
60 non-exec code chunks (e.g., '``` r')
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(infile) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* Checking for library/require of dreamlet...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 18 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/run_mash.Rd:103: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpavkwGc/file272f794106ac0b/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* 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; 415 lines (4%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1853 lines (18%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 499 lines
(5%) 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 | 1 WARNINGS | 12 NOTES
See the dreamlet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.