===============================
R CMD BUILD
===============================
* checking for file ‘beachmat.tiledb/DESCRIPTION’ ... OK
* preparing ‘beachmat.tiledb’:
* 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 ‘beachmat.tiledb_0.99.0.tar.gz’
===============================
BiocCheckGitClone('beachmat.tiledb')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3651/beachmat.tiledb_20241125154923/beachmat.tiledb
→ BiocVersion: 3.21
→ Package: beachmat.tiledb
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3651/beachmat.tiledb_20241125154923/beachmat.tiledb.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3651/beachmat.tiledb_20241125154923/beachmat.tiledb
→ 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/3651/beachmat.tiledb_20241125154923/beachmat.tiledb.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 ‘beachmat.tiledb/DESCRIPTION’ ... OK
* this is package ‘beachmat.tiledb’ 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 ‘beachmat.tiledb’ can be installed ... WARNING
Found the following significant warnings:
/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/attribute.h:488:30: warning: ‘int32_t tiledb_attribute_dump(tiledb_ctx_t*, const tiledb_attribute_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/dimension.h:409:30: warning: ‘int32_t tiledb_dimension_dump(tiledb_ctx_t*, const tiledb_dimension_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/domain.h:167:40: warning: ‘int32_t tiledb_domain_dump(tiledb_ctx_t*, const tiledb_domain_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
/home/biocbuild/bbs-3.21-bioc/R/site-library/tiledb/tiledb/include/tiledb/array_schema.h:170:33: warning: ‘int32_t tiledb_array_schema_dump(tiledb_ctx_t*, const tiledb_array_schema_t*, FILE*)’ is deprecated [-Wdeprecated-declarations]
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3651/beachmat.tiledb_20241125154923/beachmat.tiledb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 14.3Mb
sub-directories of 1Mb or more:
libs 14.2Mb
* 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [16s/16s] 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work. If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* 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 ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/10s]
[14s/11s] 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 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3651/beachmat.tiledb_20241125154923/beachmat.tiledb.Rcheck/00check.log’
for details.
===============================
BiocCheck('beachmat.tiledb_0.99.0.tar.gz')
===============================
── Installing beachmat.tiledb ──────────────────────────────────────────────────
✔ Package installed successfully
── beachmat.tiledb session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJjqMc6/file34ae58373141c/beachmat.tiledb
→ BiocVersion: 3.21
→ Package: beachmat.tiledb
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3651/beachmat.tiledb_20241125154923/beachmat.tiledb.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpJjqMc6/file34ae58373141c/beachmat.tiledb
→ installDir: /tmp/RtmpJjqMc6/file34ae589065169
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on beachmat.tiledb ────────────────────────────────────────
* 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/RtmpJjqMc6/file34ae58373141c/beachmat.tiledb//src/beachmat.tiledb.so
• ...
• /tmp/RtmpJjqMc6/file34ae58373141c/beachmat.tiledb/src/load_sparse.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...
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (50%).
* 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 beachmat.tiledb...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 52 lines (23%) are > 80 characters long.
First few lines:
• R/initializeCpp.R#L3 #' Initialize C++ representations of Til ...
• ...
• vignettes/userguide.Rmd#L48 Importing `r Biocpkg("beachmat.tiledb")` ...
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 4 NOTES
i See the beachmat.tiledb.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.