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R CMD BUILD
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* checking for file ‘MetaboDynamics/DESCRIPTION’ ... OK
* preparing ‘MetaboDynamics’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* 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 ‘MetaboDynamics_0.99.2.tar.gz’
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BiocCheckGitClone('MetaboDynamics')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3565/7008a8fd04da783573b1c7ce0c8b729eb4d2a03e/MetaboDynamics
→ BiocVersion: 3.20
→ Package: MetaboDynamics
→ PackageVersion: 0.99.2
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3565/7008a8fd04da783573b1c7ce0c8b729eb4d2a03e/MetaboDynamics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3565/7008a8fd04da783573b1c7ce0c8b729eb4d2a03e/MetaboDynamics
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• src/RcppExports.o
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3565/7008a8fd04da783573b1c7ce0c8b729eb4d2a03e/MetaboDynamics.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
* using option ‘--no-vignettes’
* checking for file ‘MetaboDynamics/DESCRIPTION’ ... OK
* this is package ‘MetaboDynamics’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MetaboDynamics’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 70.8Mb
sub-directories of 1Mb or more:
help 3.1Mb
libs 67.3Mb
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
Problems with news in ‘NEWS.md’:
No news entries found.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [25s/24s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'diagnostics_dynamics.Rd':
\examples lines wider than 100 characters:
data <- longitudinalMetabolomics[longitudinalMetabolomics$condition == "A" & longitudinalMetabolomics$metabolite == "ATP", ]
Rd file 'estimates_dynamics.Rd':
\examples lines wider than 100 characters:
data <- longitudinalMetabolomics[longitudinalMetabolomics$condition == "A" & longitudinalMetabolomics$metabolite == "ATP", ]
Rd file 'fit_dynamics_model.Rd':
\examples lines wider than 100 characters:
data <- longitudinalMetabolomics[longitudinalMetabolomics$condition == "A" & longitudinalMetabolomics$metabolite == "ATP", ]
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘longitudinalMetabolomics’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Data with usage in Rd file 'longitudinalMetabolomics.Rd' but not in code:
‘data_sim’
Warning in utils::data(list = al, envir = data_env) :
data set ‘data_sim’ not found
* 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 ... [5s/5s] OK
* checking data for ASCII and uncompressed saves ... 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 ... NOTE
GNU make is a SystemRequirements.
* 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’ ... OK
* checking examples ... [96s/98s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
compare_dynamics 64.332 0.128 64.467
ORA_hypergeometric 9.673 0.161 9.835
* 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/2s] OK
* DONE
Status: 2 WARNINGs, 5 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3565/7008a8fd04da783573b1c7ce0c8b729eb4d2a03e/MetaboDynamics.Rcheck/00check.log’
for details.
===============================
BiocCheck('MetaboDynamics_0.99.2.tar.gz')
===============================
── Installing MetaboDynamics ───────────────────────────────────────────────────
✔ Package installed successfully
── MetaboDynamics session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmptUNlhj/file1044434d53c36/MetaboDynamics
→ BiocVersion: 3.20
→ Package: MetaboDynamics
→ PackageVersion: 0.99.2
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3565/7008a8fd04da783573b1c7ce0c8b729eb4d2a03e/MetaboDynamics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmptUNlhj/file1044434d53c36/MetaboDynamics
→ installDir: /tmp/RtmptUNlhj/file104443277eb777
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MetaboDynamics ─────────────────────────────────────────
* 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...
* Checking package size...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• /tmp/RtmptUNlhj/file1044434d53c36/MetaboDynamics//inst/doc/MetaboDynamics.html
• ...
• /tmp/RtmptUNlhj/file1044434d53c36/MetaboDynamics/src/stanExports_m_cluster_distances_padded.o
* 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...
i NOTE: Consider adding these automatically suggested biocViews: Clustering
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (18%).
* Checking for pinned package versions in DESCRIPTION...
* 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...
* Checking for library/require of MetaboDynamics...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/ORA_hypergeometric.R (line 105, column 15)
• R/ORA_hypergeometric.R (line 135, column 17)
• R/stanmodels.R (line 11, column 15)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• compare_dynamics.R (line 72, column 13)
• ...
• ORA_hypergeometric.R (line 178, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
The longest 5 functions are:
• ORA_hypergeometric() (R/ORA_hypergeometric.R): 194 lines
• ...
• get_ORA_annotations() (R/get_ORA_annotations.R): 125 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: More than 1 NEWS file found. See ?news for recognition ordering.
Please remove one of the following:
• /inst/NEWS.md
• /./NEWS.md
* Checking unit tests...
i 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...
i NOTE: Consider shorter lines; 74 lines (4%) are > 80 characters long.
First few lines:
• R/compare_dynamics.R#L1 #' Comparison of metabolite dynamics clu ...
• ...
• vignettes/MetaboDynamics.Rmd#L289 retrieved from the KEGG-database the fol
...
i NOTE: Consider multiples of 4 spaces for line indents; 571 lines (33%) are
not.
First few lines:
• R/compare_dynamics.R#L38 # bind objects to function ...
• ...
• vignettes/MetaboDynamics.Rmd#L411 ggtitle("comparison of clusters") ...
i See https://contributions.bioconductor.org/r-code.html
i 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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | • 8 NOTES
i See the MetaboDynamics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.