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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_0.99.8.tar.gz
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BiocCheckGitClone('MetaboDynamics')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3565/267d53a31c82f012a8257532a80efd702e1f4bd8/MetaboDynamics
BiocVersion: 3.21
Package: MetaboDynamics
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3565/267d53a31c82f012a8257532a80efd702e1f4bd8/MetaboDynamics.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3565/267d53a31c82f012a8257532a80efd702e1f4bd8/MetaboDynamics
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3565/267d53a31c82f012a8257532a80efd702e1f4bd8/MetaboDynamics/.gitignore'
* 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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
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R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3565/267d53a31c82f012a8257532a80efd702e1f4bd8/MetaboDynamics.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* 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 0.99.8
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
* checking installed package size ... INFO
installed size is 33.0Mb
sub-directories of 1Mb or more:
help 2.9Mb
libs 29.7Mb
* 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.
* 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 ... [9s/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 ... [28s/26s] 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 ... WARNING
Data codoc mismatches from Rd file 'modules_compounds.Rd':
Variables in data frame 'modules_compounds'
Code: KEGG lower_hierarchy middle_hierarchy module_id module_name
upper_hierarchy
Docs: ...1 KEGG lower_hierarchy middle_hierarchy module_id
upper_hierarchy
* 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 ... INFO
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 ... [178s/183s] ERROR
Running examples in MetaboDynamics-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: heatmap_metabolites
> ### Title: plot heatmap from comparison of metabolite composition
> ### compare_metabolites()
> ### Aliases: heatmap_metabolites
>
> ### ** Examples
>
> data("cluster")
> comparison <- compare_metabolites(
+ clusters = cluster
+ )
> heatmap_metabolites(distances = comparison[["Jaccard"]], clusters = cluster)
Error in heatmap_metabolites(distances = comparison[["Jaccard"]], clusters = cluster) :
'distances' must be a dataframe obtained by compare_metabolites()
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
compare_dynamics 78.780 0.434 79.221
heatmap_dynamics 76.288 0.854 77.146
get_ORA_annotations 0.521 0.018 5.558
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [15s/18s]
[16s/18s] 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/3565/267d53a31c82f012a8257532a80efd702e1f4bd8/MetaboDynamics.Rcheck/00check.log
for details.
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BiocCheck('MetaboDynamics_0.99.8.tar.gz')
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Installing MetaboDynamics
Package installed successfully
MetaboDynamics session metadata
sourceDir: /tmp/Rtmp63h3c7/file216e9206d1e53/MetaboDynamics
BiocVersion: 3.21
Package: MetaboDynamics
PackageVersion: 0.99.8
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3565/267d53a31c82f012a8257532a80efd702e1f4bd8/MetaboDynamics.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/Rtmp63h3c7/file216e9206d1e53/MetaboDynamics
installDir: /tmp/Rtmp63h3c7/file216e982320e2
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...
i NOTE: Update R version dependency from 4.4.0 to 4.5.0.
* Checking package size...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
/tmp/Rtmp63h3c7/file216e9206d1e53/MetaboDynamics//inst/doc/MetaboDynamics.html
...
/tmp/Rtmp63h3c7/file216e9206d1e53/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/compare_dynamics.R (line 113, column 8)
...
R/stanmodels.R (line 11, column 15)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
compare_dynamics.R (line 118, column 17)
...
plot_estimates.R (line 97, column 24)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/get_ORA_annotations.R (line 154, column 7)
* 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 9
functions greater than 50 lines.
The longest 5 functions are:
ORA_hypergeometric() (R/ORA_hypergeometric.R): 205 lines
...
plot_diagnostics() (R/plot_diagnostics.R): 118 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 114 lines (5%) are > 80 characters long.
First few lines:
R/compare_dynamics.R#L1 #' Comparison of metabolite dynamics clu ...
...
vignettes/MetaboDynamics.Rmd#L387 heatmap_dynamics(estimates = comparison_
...
i NOTE: Consider multiples of 4 spaces for line indents; 812 lines (37%) are
not.
First few lines:
R/compare_dynamics.R#L38 # bind objects to function ...
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vignettes/MetaboDynamics.Rmd#L432 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 v1.43.2 results
0 ERRORS | 1 WARNINGS | i 8 NOTES
i See the MetaboDynamics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.