===============================
BiocCheckGitClone('CAMPP2')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: CAMPP2
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2999/CAMPP2_20230403133420/CAMPP2
─ 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...
* Checking that provided CITATION file is correctly formatted...
* NOTE: CITATION file might be not correctly formatted
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2999/CAMPP2_20230403133420/CAMPP2.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* 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 ‘CAMPP2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAMPP2’ version ‘0.99.0’
* 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 ‘CAMPP2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [27s/27s] NOTE
PCAPlot: warning in PCA(t(data), graph = FALSE, ncp = 10, scale =
scale): partial argument match of 'scale' to 'scale.unit'
runKmeans: warning in PCA(t(data), graph = FALSE, ncp = 10, scale =
pca.scale): partial argument match of 'scale' to 'scale.unit'
BatchCorrect: no visible global function definition for ‘model.matrix’
DEAFeatureApply: no visible binding for global variable ‘features’
Design.Matrix: no visible global function definition for ‘model.matrix’
ExportDEA: no visible global function definition for ‘write.table’
ForestFeatures: no visible global function definition for ‘predict’
LASSOFeature: no visible global function definition for ‘as’
LASSOFeature: no visible global function definition for ‘predict’
MakeHeatmap: no visible global function definition for ‘png’
MakeHeatmap: no visible global function definition for ‘dev.off’
MakeUpset: no visible global function definition for ‘pdf’
MakeUpset: no visible global function definition for ‘rainbow’
MakeUpset: no visible global function definition for ‘dev.off’
MakeVolcano: no visible global function definition for ‘head’
MakeVolcano: no visible global function definition for ‘tail’
MakeVolcano: no visible binding for global variable ‘logFC’
MakeVolcano: no visible binding for global variable ‘adj.P.Val’
MakeVolcano: no visible binding for global variable ‘diffexpressed’
MakeVolcano: no visible binding for global variable ‘DEAlabel’
NormalizeData: no visible global function definition for ‘model.matrix’
NormalizeData: no visible global function definition for ‘logit’
NormalizeData: no visible binding for global variable ‘median’
PlotDistributions: no visible global function definition for ‘pdf’
PlotDistributions: no visible global function definition for ‘par’
PlotDistributions: no visible global function definition for ‘dev.off’
RFApply: no visible global function definition for ‘is’
RFApply: no visible global function definition for ‘tail’
ReplaceNAs: no visible global function definition for ‘is’
RunDEA: no visible global function definition for ‘model.matrix’
RunDEA: no visible global function definition for ‘combn’
RunDEA_LASSO_consensus: no visible global function definition for ‘pdf’
RunDEA_LASSO_consensus: no visible global function definition for
‘dev.off’
RunHeatmap: no visible global function definition for ‘head’
RunHeatmap: no visible global function definition for ‘tail’
meanCounts: no visible binding for global variable ‘sd’
parseArguments: no visible global function definition for ‘is’
runCampp2: no visible binding for global variable ‘group1’
runCampp2: no visible binding for global variable ‘group2’
runCampp2: no visible binding for global variable ‘control.group1’
runCampp2: no visible binding for global variable ‘control.group2’
runCampp2: no visible binding for global variable ‘ids’
runCampp2: no visible binding for global variable ‘databatch1’
runCampp2: no visible binding for global variable ‘databatch2’
runCampp2: no visible binding for global variable ‘batch1’
runCampp2: no visible binding for global variable ‘batch2’
runCampp2: no visible binding for global variable ‘cutoff.logFC1’
runCampp2: no visible binding for global variable ‘cutoff.FDR1’
runCampp2: no visible binding for global variable ‘cutoff.logFC2’
runCampp2: no visible binding for global variable ‘cutoff.FDR2’
runCampp2: no visible binding for global variable ‘block1’
runCampp2: no visible binding for global variable ‘block2’
runCampp2: no visible binding for global variable ‘covarDEA1’
runCampp2: no visible binding for global variable ‘covarDEA2’
runCampp2: no visible binding for global variable ‘DEA.allowed.type’
runCampp2: no visible binding for global variable ‘data1.batch’
runCampp2: no visible binding for global variable ‘data2.batch’
runCampp2: no visible global function definition for ‘write.table’
runCampp2: no visible binding for global variable ‘comparison’
runKmeans: no visible global function definition for ‘png’
runKmeans: no visible global function definition for ‘dev.off’
runKmeans: no visible global function definition for ‘kmeans’
runLASSO: no visible global function definition for ‘predict’
Undefined global functions or variables:
DEA.allowed.type DEAlabel adj.P.Val as batch1 batch2 block1 block2
combn comparison control.group1 control.group2 covarDEA1 covarDEA2
cutoff.FDR1 cutoff.FDR2 cutoff.logFC1 cutoff.logFC2 data1.batch
data2.batch databatch1 databatch2 dev.off diffexpressed features
group1 group2 head ids is kmeans logFC logit median model.matrix par
pdf png predict rainbow sd tail write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf", "png", "rainbow")
importFrom("graphics", "par")
importFrom("methods", "as", "is")
importFrom("stats", "kmeans", "median", "model.matrix", "predict",
"sd")
importFrom("utils", "combn", "head", "tail", "write.table")
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 ... NOTE
Rd file 'FixZeros.Rd':
\examples lines wider than 100 characters:
FixZeros(data=campp2_brca_1_replacedNAs,group=campp2_brca_1_meta$diagnosis, remove.sparse.features=TRUE)
Rd file 'MakeUpset.Rd':
\examples lines wider than 100 characters:
campp2_brca_1_DEA_HUGO_features_per_group <- append(campp2_brca_1_DEA_HUGO_features_per_group,list(features$name))
names(campp2_brca_1_DEA_HUGO_features_per_group) <- gsub("-","",gsub(control.group,"",names(groups.full.list)))
Rd file 'MakeVennDiagram.Rd':
\examples lines wider than 100 characters:
campp2_brca_1_DEA_HUGO_features_per_group <- append(campp2_brca_1_DEA_HUGO_features_per_group,list(features$name))
names(campp2_brca_1_DEA_HUGO_features_per_group) <- gsub("-","",gsub(control.group,"",names(groups.full.list)))
Rd file 'PCAPlot.Rd':
\examples lines wider than 100 characters:
PCAPlot(campp2_brca_1_batchCorrected, as.factor(campp2_brca_1_meta$subtype), show.PCA.labels =FALSE, cols=NULL, prefix="test_PCA")
Rd file 'runCampp2.Rd':
\examples lines wider than 100 characters:
runCampp2(batches=c("tumor_stage","tumor_stage"),prefix="test_CAMPP2_distr", data1=campp2_brca_1, data2=campp2_brca_2, metadata1=campp2 ... [TRUNCATED]
Rd file 'runLASSO.Rd':
\examples lines wider than 100 characters:
campp2_test_data_LASSO_zeroFix<-FixZeros(data=campp2_test_data_LASSO_replaceNAs,group=campp2_test_metadata_LASSO$diagnosis, remove.spar ... [TRUNCATED]
campp2_test_data_LASSO_normalized<-NormalizeData(data=campp2_test_data_LASSO_zeroFix,group=campp2_test_metadata_LASSO$diagnosis,standar ... [TRUNCATED]
campp2_test_data_LASSO_batchCorrected<-BatchCorrect(data=campp2_test_data_LASSO_normalized,batch=campp2_test_metadata_LASSO$tumor_stage ... [TRUNCATED]
runLASSO(data=campp2_test_data_LASSO_batchCorrected, group=campp2_test_metadata_LASSO$diagnosis, alpha=0.5, min.coef=0, nfolds=10, pref ... [TRUNCATED]
These lines will be truncated in the PDF manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [194s/211s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runCampp2 44.904 0.712 58.016
MakeHeatmap 44.119 1.117 45.187
EstimateKmeans 19.962 9.178 29.144
runLASSO 12.774 0.060 12.834
meanCounts 8.363 0.832 9.195
RunHeatmap 6.621 0.236 6.856
AddGeneName 0.798 0.043 5.717
* 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2999/CAMPP2_20230403133420/CAMPP2.Rcheck/00check.log’
for details.
===============================
BiocCheck('CAMPP2_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: CAMPP2
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpkwinIV/file6cd54553a55bc/CAMPP2
─ installDir: /tmp/RtmpkwinIV/file6cd54519503ff
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2999/CAMPP2_20230403133420/CAMPP2.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.3.0.
* 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:
GenePrediction
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...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict 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 CAMPP2...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 10% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* 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...
* NOTE: Consider shorter lines; 771 lines (10%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 378 lines
(5%) 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 | 0 WARNINGS | 18 NOTES
See the CAMPP2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.