===============================
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_0.99.1.tar.gz
===============================
BiocCheckGitClone('h5mread')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/9f6038bd1ffd901181372f2964954996a0cdcb2e/h5mread
BiocVersion: 3.21
Package: h5mread
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/9f6038bd1ffd901181372f2964954996a0cdcb2e/h5mread.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/9f6038bd1ffd901181372f2964954996a0cdcb2e/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/3673/9f6038bd1ffd901181372f2964954996a0cdcb2e/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 0.99.1
* 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 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 ... [13s/13s] 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)
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.
See Writing portable packages in the Writing R Extensions manual.
* checking files in vignettes ... OK
* checking examples ... [65s/78s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
h5mread 51.142 6.041 66.98
* 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/3673/9f6038bd1ffd901181372f2964954996a0cdcb2e/h5mread.Rcheck/00check.log
for details.
===============================
BiocCheck('h5mread_0.99.1.tar.gz')
===============================
Installing h5mread
Package installed successfully
h5mread session metadata
sourceDir: /tmp/RtmpCuWEam/file15b44d2773eb89/h5mread
BiocVersion: 3.21
Package: h5mread
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3673/9f6038bd1ffd901181372f2964954996a0cdcb2e/h5mread.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpCuWEam/file15b44d2773eb89/h5mread
installDir: /tmp/RtmpCuWEam/file15b44d35d3118b
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/RtmpCuWEam/file15b44d2773eb89/h5mread//src/h5mread.so
/tmp/RtmpCuWEam/file15b44d2773eb89/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.