===============================
BiocCheckGitClone('bamSliceR')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3587/61e4a81edc7f338778877e712dd7c7ddda978565/bamSliceR
→ BiocVersion: 3.20
→ Package: bamSliceR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3587/61e4a81edc7f338778877e712dd7c7ddda978565/bamSliceR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3587/61e4a81edc7f338778877e712dd7c7ddda978565/bamSliceR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• BamSlicing.Rproj
* 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 ──────────────────────────────────────────────────
✖ 1 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/3587/61e4a81edc7f338778877e712dd7c7ddda978565/bamSliceR.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 ‘bamSliceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bamSliceR’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'gmapR', 'VariantAnnotation', 'GenomicRanges', 'plyranges',
'GenomicDataCommons', 'Rsamtools', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘bamSliceR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 20.2Mb
sub-directories of 1Mb or more:
extdata 19.9Mb
* 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] 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 ... [47s/47s] NOTE
Found the following possibly unsafe calls:
File ‘bamSliceR/R/tallyReads.R’:
assignInNamespace("normalizeIndelAlleles", normalizeIndelAlleles_modified,
ns = "gmapR", pos = "package:gmapR")
.find_txs_coords_by_exons: no visible global function definition for
‘seqnames’
.get_cds_from_GRanges: no visible global function definition for
‘seqnames’
.get_exons_from_GRanges: no visible global function definition for
‘seqnames’
.get_transcripts_from_GRanges: no visible global function definition
for ‘seqnames’
annotateWithBAMinfo: no visible global function definition for
‘mcols<-’
annotateWithBAMinfo: no visible global function definition for
‘sampleNames’
availableExpStrategy: no visible global function definition for
‘projects’
availableExpStrategy: no visible binding for global variable
‘project_id’
availableExpStrategy: no visible global function definition for
‘aggregations’
availableProjectId: no visible global function definition for
‘results_all’
availableProjectId: no visible global function definition for
‘projects’
availableWorkFlow: no visible global function definition for
‘available_fields’
availableWorkFlow: no visible global function definition for ‘files’
availableWorkFlow: no visible binding for global variable
‘cases.project.project_id’
availableWorkFlow: no visible binding for global variable
‘experimental_strategy’
availableWorkFlow: no visible global function definition for
‘aggregations’
fixIndelRefCounts : .local: no visible global function definition for
‘flank’
fixIndelRefCounts : .local: no visible global function definition for
‘disjoin’
fixIndelRefCounts : .local: no visible binding for global variable
‘nucleotide’
fixIndelRefCounts : .local: no visible global function definition for
‘aggregate’
fixIndelRefCounts : .local: no visible global function definition for
‘seqnames’
fixIndelRefCounts: no visible global function definition for
‘bind_ranges’
fixMissingTxs : .findMissingTxs: no visible global function definition
for ‘seqnames’
fixMissingTxs : .findMissingTxs : <anonymous>: no visible binding for
global variable ‘downloaded_file_name’
fixMissingTxs : .findMissingTxs : <anonymous>: no visible binding for
global variable ‘gp_mb_tag’
fixMissingTxs : .findMissingTxs: no visible global function definition
for ‘VRanges’
fixMissingTxs : .findMissingTxs: no visible global function definition
for ‘Rle’
fixMissingTxs : .findMissingTxs: no visible global function definition
for ‘mcols<-’
fixMissingTxs : .findMissingTxs: no visible global function definition
for ‘sampleNames’
fixMissingTxs: no visible global function definition for ‘mcols<-’
generateDummyVariants: no visible global function definition for
‘read.delim’
getDisjoinOverlapBins: no visible binding for global variable ‘type’
getDisjoinOverlapBins: no visible global function definition for
‘seqnames’
getDisjoinOverlapBins: no visible global function definition for
‘disjoin’
getDisjoinOverlapBins: no visible global function definition for
‘mcols<-’
getGDCBAMs: no visible global function definition for
‘available_fields’
getGDCBAMs: no visible global function definition for ‘files’
getGDCBAMs: no visible binding for global variable
‘cases.project.project_id’
getGDCBAMs: no visible binding for global variable
‘experimental_strategy’
getGDCBAMs: no visible binding for global variable ‘data_format’
getGDCBAMs: no visible binding for global variable
‘analysis.workflow_type’
getGDCBAMs: no visible global function definition for ‘results_all’
getGRangesGivenGeneNames: no visible global function definition for
‘TxDb<-’
getGRangesGivenGeneNames: no visible global function definition for
‘exonsBy’
getGRangesGivenGeneNames: no visible global function definition for
‘mapIds’
getGRangesGivenGeneNames : helper: no visible global function
definition for ‘ranges<-’
getGRangesGivenGeneNames: no visible global function definition for
‘GRangesList’
getGRangesGivenGeneNames: no visible global function definition for
‘seqnames’
getGenCodeAnnotation.Txs: no visible global function definition for
‘seqnames’
getGenCodeAnnotation.Txs: no visible binding for global variable
‘g_type’
getGenCodeAnnotation.Txs: no visible global function definition for
‘mcols<-’
getGenCodeAnnotation.Txs: no visible binding for global variable
‘g_strand’
getGenesCoordinates: no visible global function definition for
‘makeGRangesFromDataFrame’
getGenesCoordinates: no visible binding for global variable ‘seqnames’
getGenesCoordinates: no visible global function definition for
‘seqnames’
getHotSpot: no visible binding for global variable ‘SYMBOL’
getHotSpot: no visible binding for global variable ‘POS’
getMultiHits: no visible global function definition for ‘sampleNames’
getMultiHits: no visible global function definition for ‘mcols<-’
getMultiHits: no visible global function definition for ‘Rle’
getMultiHits: no visible binding for global variable ‘isMultiBinHits’
getMultiHits: no visible binding for global variable
‘overlapBin_query_tag’
getVEPAnnotation: no visible global function definition for ‘seqnames’
getVEPAnnotation: no visible global function definition for ‘mcols<-’
getVariantAnnotation: no visible global function definition for
‘seqlevels<-’
getVariantAnnotation: no visible global function definition for
‘mapIds’
getVariantAnnotationForTxs: no visible global function definition for
‘strand<-’
getVariantAnnotationForTxs: no visible global function definition for
‘makeTxDbFromGRanges’
getVariantAnnotationForTxs: no visible binding for global variable
‘type’
getVariantAnnotationForTxs: no visible global function definition for
‘mcols<-’
get_proteinPaint: no visible global function definition for ‘seqnames’
gr2vrforVEP: no visible global function definition for ‘VRanges’
gr2vrforVEP: no visible global function definition for ‘seqnames’
grToMAF: no visible global function definition for ‘seqnames’
keepUniquePatient: no visible global function definition for
‘GRangesList’
parseCSQ: no visible global function definition for ‘rowRanges’
parseCSQ: no visible global function definition for ‘header’
parseCSQ: no visible global function definition for ‘DataFrame’
parseCSQ: no visible global function definition for ‘mcols<-’
plotVAF: no visible binding for global variable ‘CHANGE’
plotVAF: no visible binding for global variable ‘POS’
plotVafwithGR: no visible binding for global variable ‘t_vaf’
plotVafwithGR: no visible binding for global variable ‘t_alt_count’
plotVafwithGR: no visible binding for global variable ‘t_ref_count’
plotVafwithGR: no visible global function definition for ‘.’
plotVafwithGR: no visible binding for global variable ‘Hugo_Symbol’
plotVafwithGR: no visible binding for global variable ‘value’
plotVafwithGR: no visible binding for global variable ‘V1’
sampleTypeDecoder: no visible global function definition for
‘case_when’
saveVRinfo: no visible global function definition for ‘alt’
saveVRinfo: no visible global function definition for ‘totalDepth’
saveVRinfo: no visible global function definition for ‘altDepth’
saveVRinfo: no visible global function definition for ‘mcols<-’
smartFilter: no visible binding for global variable ‘VAF’
smartFilter: no visible binding for global variable ‘altDepth’
smartFilter: no visible global function definition for ‘sampleNames’
smartFilter: no visible binding for global variable ‘tag’
tallyReads : normalizeIndelAlleles_modified: no visible global function
definition for ‘alt’
tallyReads : normalizeIndelAlleles_modified: no visible global function
definition for ‘flank’
tallyReads : normalizeIndelAlleles_modified: no visible global function
definition for ‘ref<-’
tallyReads : normalizeIndelAlleles_modified: no visible global function
definition for ‘alt<-’
tallyReads : normalizeIndelAlleles_modified: no visible global function
definition for ‘ranges<-’
tallyReads : normalizeIndelAlleles_modified: no visible global function
definition for ‘resize’
tallyReads: no visible global function definition for
‘assignInNamespace’
tallyVariantsModified,BamFile: no visible global function definition
for ‘is’
tallyVariantsModified,BamFile : tally_region: no visible global
function definition for ‘mcols<-’
tallyVariantsModified,BamFile : tally_region: no visible global
function definition for ‘%over%’
Undefined global functions or variables:
%over% . CHANGE DataFrame GRangesList Hugo_Symbol POS Rle SYMBOL
TxDb<- V1 VAF VRanges aggregate aggregations alt alt<- altDepth
analysis.workflow_type assignInNamespace available_fields bind_ranges
case_when cases.project.project_id data_format disjoin
downloaded_file_name exonsBy experimental_strategy files flank
g_strand g_type gp_mb_tag header is isMultiBinHits
makeGRangesFromDataFrame makeTxDbFromGRanges mapIds mcols<-
nucleotide overlapBin_query_tag project_id projects ranges<-
read.delim ref<- resize results_all rowRanges sampleNames seqlevels<-
seqnames strand<- t_alt_count t_ref_count t_vaf tag totalDepth type
value
Consider adding
importFrom("methods", "is")
importFrom("stats", "aggregate")
importFrom("utils", "assignInNamespace", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... [64s/69s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getGDCBAMs 10.247 0.172 14.013
* 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: 3 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3587/61e4a81edc7f338778877e712dd7c7ddda978565/bamSliceR.Rcheck/00check.log’
for details.
===============================
BiocCheck('bamSliceR_0.99.1.tar.gz')
===============================
── Installing bamSliceR ────────────────────────────────────────────────────────
✔ Package installed successfully
── bamSliceR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp25qmtd/file1571275ced8d88/bamSliceR
→ BiocVersion: 3.20
→ Package: bamSliceR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3587/61e4a81edc7f338778877e712dd7c7ddda978565/bamSliceR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmp25qmtd/file1571275ced8d88/bamSliceR
→ installDir: /tmp/Rtmp25qmtd/file1571272f49c692
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on bamSliceR ──────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 3.5.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• /tmp/Rtmp25qmtd/file1571275ced8d88/bamSliceR//inst/doc/BamSliceR.Bioc2024.html
• /tmp/Rtmp25qmtd/file1571275ced8d88/bamSliceR/inst/doc/BamSliceR.Bioc2024.html
• /tmp/Rtmp25qmtd/file1571275ced8d88/bamSliceR/inst/doc/BamSliceR.Bioc2024.html
* 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: Coverage,
Alignment, VariantAnnotation, QualityControl
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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (59%).
* 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 bamSliceR...
! WARNING: Avoid the use of 'library' or 'require' in R code
Found in files:
• library() in R/getGRangesGivenGeneNames.r (line 22, column 5)
• library() in R/getGRangesGivenGeneNames.r (line 23, column 5)
• library() in R/getVariantAnnotation.R (line 24, column 9)
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/getGDCBAMs.R (line 67, column 15)
• ...
• R/getVariantAnnotationForTxs.R (line 226, column 15)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• downloadSlicedBAMs.r (line 26, column 35)
• ...
• tallyVariants.R (line 64, column 38)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/downloadSlicedBam.r (line 47, column 5)
• ...
• print() in R/plotVAFofSNP.R (line 20, column 9)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/annotateWithBAMinfo.R (line 19, column 21)
• ...
• R/tallyVariants.R (line 75, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
• suppressWarnings() in R/getVariantAnnotationForTxs.R (line 198, column 11)
• suppressWarnings() in R/getVariantAnnotationForTxs.R (line 199, column 3)
• suppressWarnings() in R/gff.parse.utility.r (line 86, column 11)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
The longest 5 functions are:
• getMultiHits() (R/fixMissingTxs.R): 142 lines
• ...
• get_txs_coords_of_gff() (R/gff.parse.utility.r): 94 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/downloadSlicedBAM.Rd
• ...
• man/plotVAF.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• annotateWithBAMinfo.Rd
• fixMissingTxs.Rd
• plotVAF.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 340 lines (10%) are > 80 characters long.
First few lines:
• R/annotateWithBAMinfo.R#L4 #' @param tallied_reads Either GRanges o ...
• ...
• vignettes/BamSliceR.Bioc2024.Rmd#L589 model 2: Pr(V|Tx in TxCanHarborV) !=
Pr( ...
i NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
First few lines:
• R/extractBasesAtPosition.R#L19 "positions" = positions, ...
• ...
• R/getGRangesGivenGeneNames.r#L48 } ...
i NOTE: Consider multiples of 4 spaces for line indents; 1077 lines (33%) are
not.
First few lines:
• R/annotateWithBAMinfo.R#L24 file_meta ...
• ...
• vignettes/BamSliceR.Bioc2024.Rmd#L582 i = which(colnames(theta_ ...
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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/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 ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | • 15 NOTES
i See the bamSliceR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.