===============================
R CMD BUILD
===============================
* checking for file h5mread/DESCRIPTION ... OK
* preparing h5mread:
* 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
* building h5mread_0.99.0.tar.gz
===============================
BiocCheckGitClone('h5mread')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/h5mread_20241216193403/h5mread
BiocVersion: 3.21
Package: h5mread
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/h5mread_20241216193403/h5mread.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/h5mread_20241216193403/h5mread
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* 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')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3673/h5mread_20241216193403/h5mread.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 h5mread/DESCRIPTION ... OK
* this is package h5mread version 0.99.0
* 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 serialization versions ... OK
* checking whether package h5mread can be installed ... OK
* used C compiler: gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* checking installed package size ... INFO
installed size is 10.4Mb
sub-directories of 1Mb or more:
extdata 2.1Mb
libs 7.7Mb
* 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 ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking whether startup messages can be suppressed ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: rhdf5:::h5checktypeOrOpenLocS3
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [12s/12s] 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 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 ... WARNING
Note: information on .o files is not available
File /home/pkgbuild/packagebuilder/workers/jobs/3673/R-libs/h5mread/libs/h5mread.so:
Found __printf_chk, possibly from printf (C)
Found __sprintf_chk, possibly from sprintf (C)
Found abort, possibly from abort (C)
Found exit, possibly from exit (C)
Found rand_r, possibly from rand_r (C)
Found stderr, possibly from stderr (C)
Found stdout, possibly from stdout (C)
File h5mread/libs/h5mread.so:
Found no call to: R_useDynamicSymbols
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
It is good practice to register native routines and to disable symbol
search.
See Writing portable packages in the Writing R Extensions manual.
* checking files in vignettes ... OK
* checking examples ... [106s/362s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
h5mread 65.726 31.857 351.246
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [65s/65s]
[65s/65s] 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 ... [4s/4s] OK
* DONE
Status: 1 WARNING, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3673/h5mread_20241216193403/h5mread.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('h5mread_0.99.0.tar.gz')
===============================
Installing h5mread
Package installed successfully
h5mread session metadata
sourceDir: /tmp/RtmpycJVxV/file3794a637a1ba5f/h5mread
BiocVersion: 3.21
Package: h5mread
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/h5mread_20241216193403/h5mread.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpycJVxV/file3794a637a1ba5f/h5mread
installDir: /tmp/RtmpycJVxV/file3794a66541e822
isTarBall: TRUE
platform: unix
Running BiocCheck on h5mread
* 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/RtmpycJVxV/file3794a637a1ba5f/h5mread//src/h5mread.so
/tmp/RtmpycJVxV/file3794a637a1ba5f/h5mread/src/h5mread.so
* 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:
SupportVectorMachine
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 (70%).
* 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 h5mread...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/h5dim.R (line 89, column 19)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
suppressMessages() in R/h5dim.R (line 21, column 12)
suppressMessages() in R/h5dim.R (line 29, column 12)
suppressMessages() in R/h5dim.R (line 37, column 12)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
h5mread() (R/h5mread.R): 87 lines
h5mread_from_reshaped() (R/h5mread_from_reshaped.R): 56 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 33% of man
pages use at least one of these tags.
Found in files:
H5File-class.Rd
h5mread.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
H5File-class.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...
i NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long.
First few lines:
man/h5ls.Rd#L19 \item{file, recursive, all, datasetinf ...
i NOTE: Consider multiples of 4 spaces for line indents; 302 lines (13%) are
not.
First few lines:
R/h5dim.R#L88 "\n\n ", ...
...
vignettes/h5mread.Rmd#L139 identical(as.array(a22), as.array(a2)) ...
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 h5mread.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.