===============================
BiocCheckGitClone('sciCNV')
===============================
This is BiocCheckGitClone version 1.31.34. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2383/f682f66638386620bd001f97a31034a211ba4309/sciCNV.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sciCNV/DESCRIPTION’ ... OK
* this is package ‘sciCNV’ version ‘0.99.65’
* 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 ‘sciCNV’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Invalid license file pointers: LICENSE
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [5s/5s] NOTE
CNV_htmp_glist: no visible global function definition for
‘colorRampPalette’
CNV_htmp_gloc: no visible binding for global variable ‘genLoc1’
CNV_htmp_gloc: no visible global function definition for
‘colorRampPalette’
heatmap_break_gloc: no visible binding for global variable ‘genLoc1’
Undefined global functions or variables:
colorRampPalette genLoc1
Consider adding
importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'CNV_infer.Rd':
\examples lines wider than 100 characters:
iCNV_percell <- CNV_infer(ss.expr=norm_expr_percell, mean.ctrl, gen.Loc, resolution=50, chr.n, P12, mat.fab)
Rd file 'Opt_MeanSD_RTAM1.Rd':
\examples lines wider than 100 characters:
CV_for_RTAM1 <- Opt_MeanSD_RTAM1(Normalized_log=normalized_data, Order_Matrix, nGene, Min_nGene=250, gene_cutoff=250)
Rd file 'Opt_MeanSD_RTAM2.Rd':
\examples lines wider than 100 characters:
CV_for_RTAM2 <- Opt_MeanSD_RTAM2(Normalized_log=normalized_data, Order_Matrix, nGene, Min_nGene=250, gene_cutoff=250)
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘10XGenomics_gen_pos_GRCh38-1.2.0’ ‘HouseKeepingGenes’
‘Sample_CNV_matrix’ ‘Sample_breakGlist’ ‘Sample_breakGloc’
Undocumented data sets:
‘10XGenomics_gen_pos_GRCh38-1.2.0’ ‘HouseKeepingGenes’
‘Sample_CNV_matrix’ ‘Sample_breakGlist’ ‘Sample_breakGloc’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'CNV_htmp_glist'
‘clustering.type’ ‘sorting’ ‘CNVscore’ ‘cluster.lines’ ‘breakGlist’
‘No.test’
Documented arguments not in \usage in documentation object 'CNV_htmp_glist':
‘clustering.type:’ ‘sorting:’ ‘CNVscore:’ ‘cluster.lines:’
‘breakGlist:’ ‘No.test:’ ‘Gen.Loc’
Undocumented arguments in documentation object 'CNV_infer'
‘gen.Loc’
Undocumented arguments in documentation object 'CNV_score'
‘M_nf’
Documented arguments not in \usage in documentation object 'CNV_score':
‘M_nF’
Undocumented arguments in documentation object 'RTAM_normalization'
‘method’ ‘Min_nGn’ ‘Optimizing’
Documented arguments not in \usage in documentation object 'RTAM_normalization':
‘Genes’ ‘Order_Matrix’ ‘MinNumGenes’ ‘OptNumGenes’
Undocumented arguments in documentation object 'Scaling_CNV'
‘n.TestCells’ ‘scaling.factor’
Documented arguments not in \usage in documentation object 'Scaling_CNV':
‘Vn.TestCells’ ‘Vscaling.factor’
Undocumented arguments in documentation object 'Sketch_AveCNV'
‘Assoc.Chr’
Undocumented arguments in documentation object 'heatmap.3'
‘x’ ‘Rowv’ ‘Colv’ ‘distfun’ ‘hclustfun’ ‘dendrogram’ ‘symm’ ‘scale’
‘na.rm’ ‘revC’ ‘add.expr’ ‘breaks’ ‘symbreaks’ ‘col’ ‘colsep’
‘rowsep’ ‘sepcolor’ ‘sepwidth’ ‘cellnote’ ‘notecex’ ‘notecol’
‘na.color’ ‘trace’ ‘tracecol’ ‘hline’ ‘vline’ ‘linecol’ ‘margins’
‘ColSideColors’ ‘RowSideColors’ ‘side.height.fraction’ ‘cexRow’
‘cexCol’ ‘labRow’ ‘labCol’ ‘key’ ‘keysize’ ‘density.info’ ‘denscol’
‘symkey’ ‘densadj’ ‘main’ ‘xlab’ ‘ylab’ ‘lmat’ ‘lhei’ ‘lwid’
‘ColSideColorsSize’ ‘RowSideColorsSize’ ‘KeyValueName’ ‘...’
Undocumented arguments in documentation object 'sciCNV'
‘norm.mat’ ‘ave.ctrl’ ‘gen.Loc’ ‘No.test’ ‘sharpness’ ‘baseline_adj’
‘baseline’
Documented arguments not in \usage in documentation object 'sciCNV':
‘norm.mat:’ ‘ave.ctrl:’ ‘gen.Loc:’ ‘No.test:’ ‘sharpness:’
‘baseline_adj:’ ‘baseline:’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘beanplot’
'library' or 'require' calls not declared from:
‘Matrix’ ‘RColorBrewer’ ‘Rtsne’ ‘Seurat’ ‘beanplot’ ‘devtools’
‘dplyr’ ‘ggplot2’ ‘ggridges’ ‘qlcMatrix’ ‘reticulate’ ‘svd’ ‘umap’
‘viridis’
* 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 ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2383/f682f66638386620bd001f97a31034a211ba4309/sciCNV.Rcheck/00check.log’
for details.
===============================
BiocCheck('sciCNV_0.99.65.tar.gz')
===============================
This is BiocCheck version 1.31.34. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2383/f682f66638386620bd001f97a31034a211ba4309/sciCNV_0.99.65.tar.gz" "/tmp/RtmptheUWZ/file5e0a05ac77da7/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 8.9709 MB
Size Requirement: 5.0000 MB
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/Introduction.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of sciCNV...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/heatmap.3.R (line 65, column 18)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
CNV_htmp_glist.R (line 187, column 45)
CNV_htmp_gloc.R (line 192, column 32)
CNV_htmp_gloc.R (line 192, column 45)
CNV_htmp_gloc.R (line 198, column 42)
CNV_htmp_gloc.R (line 198, column 55)
CNV_htmp_gloc.R (line 203, column 12)
CNV_htmp_gloc.R (line 205, column 15)
CNV_htmp_gloc.R (line 210, column 12)
CNV_htmp_gloc.R (line 238, column 45)
CNV_htmp_gloc.R (line 257, column 42)
CNV_htmp_gloc.R (line 275, column 42)
CNV_htmp_gloc.R (line 302, column 40)
CNV_htmp_gloc.R (line 310, column 38)
CNV_htmp_gloc.R (line 349, column 45)
CNV_infer.R (line 86, column 13)
CNV_infer.R (line 107, column 12)
CNV_infer.R (line 168, column 12)
CNV_infer.R (line 231, column 12)
CNV_score.R (line 38, column 13)
CNV_score.R (line 39, column 14)
CNV_score.R (line 57, column 12)
CNV_score.R (line 58, column 14)
CNV_score.R (line 68, column 9)
CNV_score.R (line 68, column 79)
CNV_score.R (line 70, column 40)
heatmap_break_glist.R (line 32, column 12)
heatmap_break_gloc.R (line 35, column 12)
heatmap_break_gloc.R (line 53, column 32)
heatmap_break_gloc.R (line 53, column 45)
heatmap_break_gloc.R (line 58, column 42)
heatmap_break_gloc.R (line 58, column 55)
heatmap_break_gloc.R (line 63, column 12)
heatmap_break_gloc.R (line 65, column 16)
heatmap_break_gloc.R (line 75, column 38)
heatmap_break_gloc.R (line 75, column 57)
heatmap.3.R (line 183, column 15)
heatmap.3.R (line 193, column 8)
heatmap.3.R (line 198, column 8)
heatmap.3.R (line 276, column 19)
heatmap.3.R (line 300, column 19)
heatmap.3.R (line 330, column 14)
heatmap.3.R (line 331, column 9)
heatmap.3.R (line 331, column 15)
heatmap.3.R (line 341, column 11)
heatmap.3.R (line 341, column 17)
heatmap.3.R (line 344, column 11)
heatmap.3.R (line 371, column 13)
Mito_umi_gn.R (line 57, column 52)
Mito_umi_gn.R (line 65, column 42)
Mito_umi_gn.R (line 85, column 39)
Mito_umi_gn.R (line 85, column 71)
Mito_umi_gn.R (line 95, column 44)
Mito_umi_gn.R (line 103, column 44)
Opt_MeanSD_RTAM1.R (line 43, column 12)
Opt_MeanSD_RTAM1.R (line 48, column 14)
Opt_MeanSD_RTAM1.R (line 67, column 13)
Opt_MeanSD_RTAM1.R (line 70, column 14)
Opt_MeanSD_RTAM1.R (line 120, column 12)
Opt_MeanSD_RTAM1.R (line 130, column 12)
Opt_MeanSD_RTAM1.R (line 131, column 14)
Opt_MeanSD_RTAM1.R (line 139, column 12)
Opt_MeanSD_RTAM1.R (line 149, column 12)
Opt_MeanSD_RTAM2.R (line 46, column 12)
Opt_MeanSD_RTAM2.R (line 51, column 14)
Opt_MeanSD_RTAM2.R (line 66, column 12)
Opt_MeanSD_RTAM2.R (line 71, column 14)
Opt_MeanSD_RTAM2.R (line 84, column 12)
Opt_MeanSD_RTAM2.R (line 89, column 14)
Opt_MeanSD_RTAM2.R (line 113, column 12)
Opt_MeanSD_RTAM2.R (line 115, column 15)
Opt_MeanSD_RTAM2.R (line 124, column 12)
Opt_MeanSD_RTAM2.R (line 125, column 14)
Opt_MeanSD_RTAM2.R (line 134, column 12)
Opt_MeanSD_RTAM2.R (line 144, column 12)
RTAM_normalization.R (line 80, column 12)
RTAM_normalization.R (line 91, column 12)
RTAM_normalization.R (line 95, column 14)
RTAM_normalization.R (line 107, column 12)
RTAM_normalization.R (line 142, column 14)
RTAM_normalization.R (line 145, column 16)
RTAM_normalization.R (line 157, column 15)
RTAM_normalization.R (line 160, column 16)
RTAM_normalization.R (line 191, column 22)
RTAM_normalization.R (line 191, column 60)
RTAM_normalization.R (line 202, column 22)
RTAM_normalization.R (line 202, column 60)
RTAM_normalization.R (line 243, column 14)
RTAM_normalization.R (line 245, column 17)
RTAM_normalization.R (line 254, column 14)
RTAM_normalization.R (line 255, column 16)
RTAM_normalization.R (line 266, column 14)
RTAM_normalization.R (line 305, column 14)
RTAM_normalization.R (line 311, column 14)
RTAM_normalization.R (line 312, column 16)
RTAM_normalization.R (line 329, column 12)
Scaling_CNV.R (line 52, column 12)
Scaling_CNV.R (line 78, column 14)
sciCNV.R (line 156, column 34)
Sketch_AveCNV.R (line 43, column 12)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/CNV_infer.R (line 51, column 18)
R/heatmap.3.R (line 249, column 11)
R/heatmap.3.R (line 279, column 11)
R/heatmap.3.R (line 280, column 18)
R/heatmap.3.R (line 281, column 17)
R/heatmap.3.R (line 282, column 13)
R/heatmap.3.R (line 284, column 27)
R/heatmap.3.R (line 285, column 30)
R/heatmap.3.R (line 286, column 15)
R/heatmap.3.R (line 288, column 11)
R/heatmap.3.R (line 303, column 11)
R/heatmap.3.R (line 304, column 18)
R/heatmap.3.R (line 305, column 17)
R/heatmap.3.R (line 306, column 13)
R/heatmap.3.R (line 308, column 27)
R/heatmap.3.R (line 309, column 30)
R/heatmap.3.R (line 310, column 15)
R/heatmap.3.R (line 312, column 11)
R/RTAM_normalization.R (line 49, column 16)
R/sciCNV.R (line 59, column 18)
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE (found 2
times)
F in R/heatmap.3.R (line 279, column 43)
F in R/heatmap.3.R (line 303, column 42)
* WARNING: Avoid class membership checks with class() / is() and ==
/ !=; Use is(x, 'class') for S4 classes
Found in files:
heatmap.3.R (line 229, column 18)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 13 functions > 50 lines.
The longest 5 functions are:
heatmap.3() (R/heatmap.3.R, line 11): 449 lines
CNV_htmp_gloc() (R/CNV_htmp_gloc.R, line 41): 398 lines
RTAM_normalization() (R/RTAM_normalization.R, line 27): 314
lines
CNV_htmp_glist() (R/CNV_htmp_glist.R, line 38): 247 lines
CNV_infer() (R/CNV_infer.R, line 34): 215 lines
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples. The following pages do not:
CNV_htmp_glist.Rd, CNV_htmp_gloc.Rd, CNV_infer.Rd, CNV_score.Rd,
heatmap_break_glist.Rd, heatmap_break_gloc.Rd, heatmap.3.Rd,
Mito_umi_gn.Rd, Opt_MeanSD_RTAM1.Rd, Opt_MeanSD_RTAM2.Rd,
RTAM_normalization.Rd, Scaling_CNV.Rd, sciCNV.Rd, Sketch_AveCNV.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
93% of man pages use one of these cases.
Found in the following files:
CNV_htmp_glist.Rd
CNV_htmp_gloc.Rd
CNV_infer.Rd
CNV_score.Rd
heatmap_break_glist.Rd
heatmap_break_gloc.Rd
Mito_umi_gn.Rd
Opt_MeanSD_RTAM1.Rd
Opt_MeanSD_RTAM2.Rd
RTAM_normalization.Rd
Scaling_CNV.Rd
sciCNV.Rd
Sketch_AveCNV.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
CNV_htmp_glist.Rd
CNV_htmp_gloc.Rd
CNV_infer.Rd
CNV_score.Rd
heatmap_break_glist.Rd
heatmap_break_gloc.Rd
Mito_umi_gn.Rd
Opt_MeanSD_RTAM1.Rd
Opt_MeanSD_RTAM2.Rd
RTAM_normalization.Rd
Scaling_CNV.Rd
sciCNV.Rd
Sketch_AveCNV.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 332 lines (8%) are > 80 characters
long.
First 6 lines:
R/CNV_htmp_glist.R:5 #' @description Generates a heatmap of single cell...
R/CNV_htmp_glist.R:8 #' @param Gen.Loc Genomic Location matrix with lis...
R/CNV_htmp_glist.R:9 #' @param clustering a TRUE/FALSE variable specify...
R/CNV_htmp_glist.R:10 #' @param clustering.type: variable specifying th...
R/CNV_htmp_glist.R:11 #' "euclidean", " spearman", ... "original...
R/CNV_htmp_glist.R:12 #' Default is "pearson". However this is ...
* NOTE: Consider multiples of 4 spaces for line indents, 1532
lines(39%) are not.
First 6 lines:
R/CNV_htmp_glist.R:39 clustering = FALSE, ...
R/CNV_htmp_glist.R:40 clustering.type = c("p...
R/CNV_htmp_glist.R:41 sorting = FALSE, ...
R/CNV_htmp_glist.R:42 CNVscore = NULL, ...
R/CNV_htmp_glist.R:43 cluster.lines = NULL,
R/CNV_htmp_glist.R:44 breakGlist, # sepa...
See http://bioconductor.org/developers/how-to/coding-style/
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: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/ .
Summary:
ERROR count: 4
WARNING count: 2
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.