===============================
R CMD BUILD
===============================
* checking for file ‘SparseArray/DESCRIPTION’ ... OK
* preparing ‘SparseArray’:
* 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 ‘SparseArray_0.99.4.tar.gz’
===============================
BiocCheckGitClone('SparseArray')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: SparseArray
─ PackageVersion: 0.99.4
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2978/f9c5eaf26bd7ce8b2233085f1c5018ceb76ca539/SparseArray
─ 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...
─ 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/2978/f9c5eaf26bd7ce8b2233085f1c5018ceb76ca539/SparseArray.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84269)
* 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 ‘SparseArray/DESCRIPTION’ ... OK
* this is package ‘SparseArray’ version ‘0.99.4’
* 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 ‘SparseArray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... [3s/3s] 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 ... [3s/3s] OK
* checking startup messages can be suppressed ... [3s/3s] 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 ... [14s/14s] 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 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
File ‘SparseArray/libs/SparseArray.so’:
Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’
File ‘SparseArray/libs/SparseArray.so’:
Found no call to: ‘R_useDynamicSymbols’
Compiled code should not call non-API entry points in R.
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 ... [29s/29s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SVT_SparseArray-class 8.833 1.425 10.258
rowsum-methods 6.183 0.457 6.640
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[8s/8s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2978/f9c5eaf26bd7ce8b2233085f1c5018ceb76ca539/SparseArray.Rcheck/00check.log’
for details.
===============================
BiocCheck('SparseArray_0.99.4.tar.gz')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: SparseArray
─ PackageVersion: 0.99.4
─ sourceDir: /tmp/RtmpSUpIl5/file2af6ae685b0c6c/SparseArray
─ installDir: /tmp/RtmpSUpIl5/file2af6ae62618d8a
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2978/f9c5eaf26bd7ce8b2233085f1c5018ceb76ca539/SparseArray.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...
* 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:
ATACSeq, RNASeq
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...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SparseArray...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/SVT_SparseArray-class.Rd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* 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; 12 lines (0%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 564 lines
(10%) 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 | 10 NOTES
See the SparseArray.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.