===============================
R CMD BUILD
===============================
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* preparing ‘scrapper’:
* 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 ‘scrapper_0.99.1.tar.gz’
===============================
BiocCheckGitClone('scrapper')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3536/ca6019cb8d7f8970521329b40784ddbd28b4e850/scrapper
→ BiocVersion: 3.20
→ Package: scrapper
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3536/ca6019cb8d7f8970521329b40784ddbd28b4e850/scrapper.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3536/ca6019cb8d7f8970521329b40784ddbd28b4e850/scrapper
→ 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3536/ca6019cb8d7f8970521329b40784ddbd28b4e850/scrapper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ 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 ‘scrapper’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
installed size is 105.6Mb
sub-directories of 1Mb or more:
libs 105.4Mb
* 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 ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/35s]
[11s/36s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
4. ├─MatrixGenerics::rowVars(x)
5. └─MatrixGenerics::rowVars(x)
6. └─MatrixGenerics:::.load_next_suggested_package_to_search(x)
── Error ('test-modelGeneVariances.R:36:9'): modelGeneVariances works with blocking ──
Error in `MatrixGenerics:::.load_next_suggested_package_to_search(x)`: Failed to find a rowVars() method for dgCMatrix objects.
However, the following packages are likely to contain the missing method
but are not installed: sparseMatrixStats, DelayedMatrixStats.
Please install them (with 'BiocManager::install(...)') and try again.
Alternatively, if you know where the missing method is defined, install
only that package.
Backtrace:
▆
1. ├─testthat::expect_equal(current$variances, rowVars(sub)) at test-modelGeneVariances.R:36:9
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─MatrixGenerics::rowVars(sub)
5. └─MatrixGenerics::rowVars(sub)
6. └─MatrixGenerics:::.load_next_suggested_package_to_search(x)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 617 ]
Error: Test failures
Execution halted
* 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, 2 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3536/ca6019cb8d7f8970521329b40784ddbd28b4e850/scrapper.Rcheck/00check.log’
for details.
===============================
BiocCheck('scrapper_0.99.1.tar.gz')
===============================
── Installing scrapper ─────────────────────────────────────────────────────────
✔ Package installed successfully
── scrapper session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmprzfktI/file80b6535b7b06b/scrapper
→ BiocVersion: 3.20
→ Package: scrapper
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3536/ca6019cb8d7f8970521329b40784ddbd28b4e850/scrapper.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmprzfktI/file80b6535b7b06b/scrapper
→ installDir: /tmp/RtmprzfktI/file80b655dbcd1e0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scrapper ───────────────────────────────────────────────
* 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/RtmprzfktI/file80b6535b7b06b/scrapper//src/compute_clrm1_factors.o
• ...
• /tmp/RtmprzfktI/file80b6535b7b06b/scrapper/src/scrapper.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: WorkflowStep
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...
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 (43%).
* 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 scrapper...
* Checking coding practice...
! WARNING: Remove set.seed usage (found 2 times)
• set.seed() in R/clusterGraph.R (line 61, column 17)
• set.seed() in R/clusterGraph.R (line 63, column 5)
* 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 3
functions greater than 50 lines.
The longest 5 functions are:
• runAllNeighborSteps() (R/runAllNeighborSteps.R): 108 lines
• scoreMarkers() (R/scoreMarkers.R): 62 lines
• modelGeneVariances() (R/modelGeneVariances.R): 60 lines
* 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; 411 lines (18%) are > 80 characters long.
First few lines:
• R/adt_quality_control.R#L4 #' and use the metrics to suggest filter ...
• ...
• vignettes/userguide.Rmd#L221 To normalize, we use size factors define ...
i NOTE: Consider multiples of 4 spaces for line indents; 2 lines (0%) are not.
First few lines:
• R/scaleByNeighbors.R#L56 scaling = scaling, ...
• R/scaleByNeighbors.R#L57 combined = do.call(rbind, x) ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | • 7 NOTES
i See the scrapper.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.