nebbiolo1 Summary
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Package: CBNplot |
Version: 0.99.2 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data CBNplot |
BuildTime: 1 minutes 10.80 seconds |
CheckCommand: BiocCheckGitClone('CBNplot') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings CBNplot_0.99.2.tar.gz && BiocCheck('CBNplot_0.99.2.tar.gz', `new-package`=TRUE) |
CheckTime: 2 minutes 52.91 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 594.23 KiB |
BuildID:: CBNplot_20220301155044 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: CBNplot. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘CBNplot/DESCRIPTION’ ... OK
* preparing ‘CBNplot’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘CBNplot_0.99.2.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('CBNplot')
===============================
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/2477/20ef69e82652860d1f8edb8ce29fbb33dc77264a/CBNplot.Rcheck’
* using R Under development (unstable) (2022-02-17 r81757)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CBNplot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CBNplot’ version ‘0.99.2’
* 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 ‘CBNplot’ can be installed ... [19s/19s] OK
* checking installed package size ... OK
* 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 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 ... [22s/22s] NOTE
bngeneplot: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bngeneplotCustom: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bnpathplot: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bnpathplotCustom: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bngeneplot: no visible binding for global variable ‘cell_line’
bngeneplot: no visible binding for global variable ‘dependency’
bngeneplot: no visible binding for global variable ‘..count..’
bngeneplot: no visible binding for global variable ‘SYMBOL’
bngeneplot: no visible binding for global variable ‘Pathway’
bngeneplot: no visible binding for global variable ‘direction’
bngeneplot: no visible binding for global variable ‘label’
bngeneplot: no visible binding for global variable ‘value’
bngeneplot: no visible binding for global variable ‘name’
bngeneplot: no visible global function definition for ‘strength.viewer’
bngeneplot: no visible binding for global variable ‘gene_name’
bngeneplot : <anonymous>: no visible binding for global variable
‘gene_name’
bngeneplot: no visible binding for global variable ‘depmap_id’
bngeneplot: no visible binding for global variable ‘lineage’
bngeneplotCustom: no visible binding for global variable ‘cell_line’
bngeneplotCustom: no visible binding for global variable ‘direction’
bngeneplotCustom: no visible binding for global variable ‘label’
bngeneplotCustom: no visible binding for global variable ‘value’
bngeneplotCustom: no visible binding for global variable ‘name’
bngeneplotCustom: no visible binding for global variable ‘gene_name’
bngeneplotCustom : <anonymous>: no visible binding for global variable
‘gene_name’
bngeneplotCustom : <anonymous>: no visible binding for global variable
‘cls’
bnpathplot: no visible binding for global variable ‘cell_line’
bnpathplot: no visible binding for global variable ‘dependency’
bnpathplot: no visible binding for global variable ‘..count..’
bnpathplot: no visible binding for global variable ‘qvalue’
bnpathplot: no visible binding for global variable ‘p.adjust’
bnpathplot: no visible binding for global variable ‘gene_name’
bnpathplot: no visible global function definition for ‘prcomp’
bnpathplot: no visible global function definition for ‘cor’
bnpathplot: no visible binding for global variable ‘direction’
bnpathplot: no visible binding for global variable ‘label’
bnpathplot: no visible binding for global variable ‘value’
bnpathplot: no visible binding for global variable ‘name’
bnpathplot: no visible global function definition for ‘strength.viewer’
bnpathplot : <anonymous>: no visible binding for global variable
‘Description’
bnpathplotCustom: no visible binding for global variable ‘cell_line’
bnpathplotCustom: no visible binding for global variable ‘qvalue’
bnpathplotCustom: no visible binding for global variable ‘p.adjust’
bnpathplotCustom: no visible binding for global variable ‘gene_name’
bnpathplotCustom: no visible global function definition for ‘prcomp’
bnpathplotCustom: no visible global function definition for ‘cor’
bnpathplotCustom: no visible binding for global variable ‘direction’
bnpathplotCustom: no visible binding for global variable ‘label’
bnpathplotCustom: no visible binding for global variable ‘value’
bnpathplotCustom: no visible binding for global variable ‘name’
bnpathplotCustom : <anonymous>: no visible binding for global variable
‘Description’
bnpathtest: no visible binding for global variable ‘qvalue’
bnpathtest: no visible binding for global variable ‘p.adjust’
bnpathtest: no visible global function definition for ‘prcomp’
queryCpDistLs: no visible binding for global variable ‘level’
queryCpDistLs: no visible binding for global variable ‘freq’
queryCpDistLs: no visible binding for global variable ‘label’
queryCpDistLw: no visible binding for global variable ‘weights’
Undefined global functions or variables:
..count.. Description Pathway SYMBOL cell_line cls cor dependency
depmap_id direction freq gene_name label level lineage name p.adjust
prcomp qvalue strength.viewer value weights
Consider adding
importFrom("stats", "cor", "p.adjust", "prcomp", "weights")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'bngeneplot.Rd':
\examples lines wider than 100 characters:
res <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, convertSymbol = TRUE, expRow = "ENSEMBL")
Rd file 'bngeneplotCustom.Rd':
\examples lines wider than 100 characters:
res <- bngeneplotCustom(results=exampleEaRes, exp=exampleGeneExp, chooseDir=TRUE, pathNum=1, glowEdgeNum=NULL, hub=3, R=40, fontFamily= ... [TRUNCATED]
Rd file 'bngenetest.Rd':
\examples lines wider than 100 characters:
res <- bngenetest(results = exampleEaRes, exp = exampleGeneExp, algo="hc", Rrange=seq(10, 30, 10), pathNum=1, scoreType="bge")
Rd file 'bnpathplotCustom.Rd':
\examples lines wider than 100 characters:
res <- bnpathplotCustom(results=exampleEaRes, exp=exampleGeneExp, fontFamily="sans", glowEdgeNum=3, hub=3)
Rd file 'bnpathtest.Rd':
\examples lines wider than 100 characters:
res <- bnpathtest(results = exampleEaRes, exp = exampleGeneExp, algo="hc", Rrange=seq(10, 30, 10), expRow = "ENSEMBL", scoreType="bge")
Rd file 'compareBNs.Rd':
\examples lines wider than 100 characters:
net1 <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, returnNet=TRUE)
net2 <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, returnNet=TRUE)
Rd file 'queryCpDistLs.Rd':
\examples lines wider than 100 characters:
## Not run: queryCpDistLs(fitted, candidate="Mitotic Spindle Checkpoint", evidences=c("TP53<0.5","TP53>0.5","TP53>0.8"), n=5000)
Rd file 'queryCpDistLw.Rd':
\examples lines wider than 100 characters:
## Not run: queryCpDistLw(fitted, candidate="COL25A1", evidence = "Treatment", level=rownames(fitted$Treatment$prob))
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
* 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 ... OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2477/20ef69e82652860d1f8edb8ce29fbb33dc77264a/CBNplot.Rcheck/00check.log’
for details.
===============================
BiocCheck('CBNplot_0.99.2.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/2477/20ef69e82652860d1f8edb8ce29fbb33dc77264a/CBNplot_0.99.2.tar.gz" "/tmp/Rtmpw8rMNC/file3f0ce216da1c94/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...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* 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:
NetworkEnrichment
See http://bioconductor.org/developers/how-to/biocViews/
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CBNplot...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/bngeneplot.R (line 73, column 39)
R/bngeneplot.R (line 95, column 31)
R/bngeneplot.R (line 96, column 39)
R/bngeneplot.R (line 101, column 31)
R/bngeneplot.R (line 373, column 26)
R/bngeneplot.R (line 374, column 27)
R/bngeneplot.R (line 464, column 26)
R/bngeneplotCustom.R (line 75, column 39)
R/bngeneplotCustom.R (line 97, column 31)
R/bnpathplot.R (line 78, column 38)
R/bnpathplot.R (line 80, column 38)
R/bnpathplot.R (line 86, column 27)
R/bnpathplot.R (line 88, column 27)
R/bnpathplot.R (line 119, column 39)
R/bnpathplot.R (line 139, column 31)
R/bnpathplot.R (line 198, column 13)
R/bnpathplot.R (line 203, column 21)
R/bnpathplot.R (line 224, column 34)
R/bnpathplot.R (line 342, column 21)
R/bnpathplot.R (line 343, column 30)
R/bnpathplot.R (line 344, column 31)
R/bnpathplot.R (line 351, column 21)
R/bnpathplot.R (line 352, column 30)
R/bnpathplot.R (line 353, column 31)
R/bnpathplot.R (line 371, column 29)
R/bnpathplot.R (line 373, column 29)
R/bnpathplot.R (line 375, column 29)
R/bnpathplotCustom.R (line 74, column 39)
R/bnpathplotCustom.R (line 83, column 23)
R/bnpathplotCustom.R (line 85, column 23)
R/bnpathplotCustom.R (line 101, column 31)
R/bnpathplotCustom.R (line 118, column 13)
R/bnpathplotCustom.R (line 123, column 21)
R/bnpathplotCustom.R (line 147, column 34)
R/bnpathplotCustom.R (line 268, column 17)
R/bnpathplotCustom.R (line 269, column 26)
R/bnpathplotCustom.R (line 270, column 27)
R/bnpathplotCustom.R (line 273, column 17)
R/bnpathplotCustom.R (line 274, column 26)
R/bnpathplotCustom.R (line 275, column 27)
R/utilities.R (line 192, column 9)
R/utilities.R (line 229, column 39)
R/utilities.R (line 321, column 39)
R/utilities.R (line 425, column 12)
R/utilities.R (line 426, column 10)
R/utilities.R (line 427, column 13)
R/utilities.R (line 428, column 13)
R/utilities.R (line 430, column 17)
R/utilities.R (line 432, column 15)
R/utilities.R (line 433, column 11)
R/utilities.R (line 436, column 23)
R/utilities.R (line 438, column 23)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
suppressMessages() in R/bnpathplot.R (line 206, column 27)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
bngeneplot() (R/bngeneplot.R, line 63): 463 lines
bnpathplot() (R/bnpathplot.R, line 64): 395 lines
bnpathplotCustom() (R/bnpathplotCustom.R, line 61): 320 lines
bngeneplotCustom() (R/bngeneplotCustom.R, line 62): 298 lines
bnpathtest() (R/utilities.R, line 226): 63 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
queryCpDistLs.Rd, queryCpDistLw.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
15% of man pages use one of these cases.
Found in the following files:
queryCpDistLs.Rd
queryCpDistLw.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
queryCpDistLs.Rd
queryCpDistLw.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; 355 lines (11%) are > 80 characters
long.
First 6 lines:
R/bngeneplot.R:5 #' @param results the enrichment analysis result from ...
R/bngeneplot.R:8 #' @param expSample candidate samples to be included i...
R/bngeneplot.R:9 #' @param algo structure learning method used in boot....
R/bngeneplot.R:10 #' @param algorithm.args parameters to pass to bnlear...
R/bngeneplot.R:12 #' @param pathNum the pathway number (the number of r...
R/bngeneplot.R:13 #' @param convertSymbol whether the label of resultin...
* NOTE: Consider multiples of 4 spaces for line indents, 398
lines(12%) are not.
First 6 lines:
R/bngeneplot.R:109 axis.text = element_text(size=10),
R/bngeneplot.R:110 axis.title = element_text(size=12))
R/bngeneplot.R:132 # rn <- clusterProfiler::bitr(rownames(pcs),
R/bngeneplot.R:133 # fromType=exp...
R/bngeneplot.R:134 # toType="SYMB...
R/bngeneplot.R:135 # OrgDb=org.Hs...
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...
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 10
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
nebbiolo1 BUILD BIN output
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merida1 Summary
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Package: CBNplot |
Version: 0.99.2 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CBNplot |
BuildTime: 1 minutes 53.43 seconds |
CheckCommand: BiocCheckGitClone('CBNplot') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CBNplot_0.99.2.tar.gz && BiocCheck('CBNplot_0.99.2.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 58.16 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh CBNplot_0.99.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 26.55 seconds |
PackageFileSize: 568.11 KiB |
BuildID:: CBNplot_20220301155044 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: CBNplot. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘CBNplot/DESCRIPTION’ ... OK
* preparing ‘CBNplot’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘CBNplot_0.99.2.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('CBNplot')
===============================
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 ‘/Users/pkgbuild/packagebuilder/workers/jobs/2477/20ef69e82652860d1f8edb8ce29fbb33dc77264a/CBNplot.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CBNplot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CBNplot’ version ‘0.99.2’
* 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 ‘CBNplot’ can be installed ... [27s/27s] OK
* checking installed package size ... OK
* 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 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 ... [28s/28s] NOTE
bngeneplot: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bngeneplotCustom: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bnpathplot: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bnpathplotCustom: warning in coord_flip(y = c(min(strengthTop$strength,
strengthTop$direction) - 0.05, 1)): partial argument match of 'y' to
'ylim'
bngeneplot: no visible binding for global variable ‘cell_line’
bngeneplot: no visible binding for global variable ‘dependency’
bngeneplot: no visible binding for global variable ‘..count..’
bngeneplot: no visible binding for global variable ‘SYMBOL’
bngeneplot: no visible binding for global variable ‘Pathway’
bngeneplot: no visible binding for global variable ‘direction’
bngeneplot: no visible binding for global variable ‘label’
bngeneplot: no visible binding for global variable ‘value’
bngeneplot: no visible binding for global variable ‘name’
bngeneplot: no visible global function definition for ‘strength.viewer’
bngeneplot: no visible binding for global variable ‘gene_name’
bngeneplot : <anonymous>: no visible binding for global variable
‘gene_name’
bngeneplot: no visible binding for global variable ‘depmap_id’
bngeneplot: no visible binding for global variable ‘lineage’
bngeneplotCustom: no visible binding for global variable ‘cell_line’
bngeneplotCustom: no visible binding for global variable ‘direction’
bngeneplotCustom: no visible binding for global variable ‘label’
bngeneplotCustom: no visible binding for global variable ‘value’
bngeneplotCustom: no visible binding for global variable ‘name’
bngeneplotCustom: no visible binding for global variable ‘gene_name’
bngeneplotCustom : <anonymous>: no visible binding for global variable
‘gene_name’
bngeneplotCustom : <anonymous>: no visible binding for global variable
‘cls’
bnpathplot: no visible binding for global variable ‘cell_line’
bnpathplot: no visible binding for global variable ‘dependency’
bnpathplot: no visible binding for global variable ‘..count..’
bnpathplot: no visible binding for global variable ‘qvalue’
bnpathplot: no visible binding for global variable ‘p.adjust’
bnpathplot: no visible binding for global variable ‘gene_name’
bnpathplot: no visible global function definition for ‘prcomp’
bnpathplot: no visible global function definition for ‘cor’
bnpathplot: no visible binding for global variable ‘direction’
bnpathplot: no visible binding for global variable ‘label’
bnpathplot: no visible binding for global variable ‘value’
bnpathplot: no visible binding for global variable ‘name’
bnpathplot: no visible global function definition for ‘strength.viewer’
bnpathplot : <anonymous>: no visible binding for global variable
‘Description’
bnpathplotCustom: no visible binding for global variable ‘cell_line’
bnpathplotCustom: no visible binding for global variable ‘qvalue’
bnpathplotCustom: no visible binding for global variable ‘p.adjust’
bnpathplotCustom: no visible binding for global variable ‘gene_name’
bnpathplotCustom: no visible global function definition for ‘prcomp’
bnpathplotCustom: no visible global function definition for ‘cor’
bnpathplotCustom: no visible binding for global variable ‘direction’
bnpathplotCustom: no visible binding for global variable ‘label’
bnpathplotCustom: no visible binding for global variable ‘value’
bnpathplotCustom: no visible binding for global variable ‘name’
bnpathplotCustom : <anonymous>: no visible binding for global variable
‘Description’
bnpathtest: no visible binding for global variable ‘qvalue’
bnpathtest: no visible binding for global variable ‘p.adjust’
bnpathtest: no visible global function definition for ‘prcomp’
queryCpDistLs: no visible binding for global variable ‘level’
queryCpDistLs: no visible binding for global variable ‘freq’
queryCpDistLs: no visible binding for global variable ‘label’
queryCpDistLw: no visible binding for global variable ‘weights’
Undefined global functions or variables:
..count.. Description Pathway SYMBOL cell_line cls cor dependency
depmap_id direction freq gene_name label level lineage name p.adjust
prcomp qvalue strength.viewer value weights
Consider adding
importFrom("stats", "cor", "p.adjust", "prcomp", "weights")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'bngeneplot.Rd':
\examples lines wider than 100 characters:
res <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, convertSymbol = TRUE, expRow = "ENSEMBL")
Rd file 'bngeneplotCustom.Rd':
\examples lines wider than 100 characters:
res <- bngeneplotCustom(results=exampleEaRes, exp=exampleGeneExp, chooseDir=TRUE, pathNum=1, glowEdgeNum=NULL, hub=3, R=40, fontFamily= ... [TRUNCATED]
Rd file 'bngenetest.Rd':
\examples lines wider than 100 characters:
res <- bngenetest(results = exampleEaRes, exp = exampleGeneExp, algo="hc", Rrange=seq(10, 30, 10), pathNum=1, scoreType="bge")
Rd file 'bnpathplotCustom.Rd':
\examples lines wider than 100 characters:
res <- bnpathplotCustom(results=exampleEaRes, exp=exampleGeneExp, fontFamily="sans", glowEdgeNum=3, hub=3)
Rd file 'bnpathtest.Rd':
\examples lines wider than 100 characters:
res <- bnpathtest(results = exampleEaRes, exp = exampleGeneExp, algo="hc", Rrange=seq(10, 30, 10), expRow = "ENSEMBL", scoreType="bge")
Rd file 'compareBNs.Rd':
\examples lines wider than 100 characters:
net1 <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, returnNet=TRUE)
net2 <- bngeneplot(results = exampleEaRes, exp = exampleGeneExp, pathNum = 1, R = 10, returnNet=TRUE)
Rd file 'queryCpDistLs.Rd':
\examples lines wider than 100 characters:
## Not run: queryCpDistLs(fitted, candidate="Mitotic Spindle Checkpoint", evidences=c("TP53<0.5","TP53>0.5","TP53>0.8"), n=5000)
Rd file 'queryCpDistLw.Rd':
\examples lines wider than 100 characters:
## Not run: queryCpDistLw(fitted, candidate="COL25A1", evidence = "Treatment", level=rownames(fitted$Treatment$prob))
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] OK
* 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 ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2477/20ef69e82652860d1f8edb8ce29fbb33dc77264a/CBNplot.Rcheck/00check.log’
for details.
===============================
BiocCheck('CBNplot_0.99.2.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 '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2477/20ef69e82652860d1f8edb8ce29fbb33dc77264a/CBNplot_0.99.2.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpodss8H/file45c57fe8c133/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...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* 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:
NetworkEnrichment
See http://bioconductor.org/developers/how-to/biocViews/
* 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...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CBNplot...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/bngeneplot.R (line 73, column 39)
R/bngeneplot.R (line 95, column 31)
R/bngeneplot.R (line 96, column 39)
R/bngeneplot.R (line 101, column 31)
R/bngeneplot.R (line 373, column 26)
R/bngeneplot.R (line 374, column 27)
R/bngeneplot.R (line 464, column 26)
R/bngeneplotCustom.R (line 75, column 39)
R/bngeneplotCustom.R (line 97, column 31)
R/bnpathplot.R (line 78, column 38)
R/bnpathplot.R (line 80, column 38)
R/bnpathplot.R (line 86, column 27)
R/bnpathplot.R (line 88, column 27)
R/bnpathplot.R (line 119, column 39)
R/bnpathplot.R (line 139, column 31)
R/bnpathplot.R (line 198, column 13)
R/bnpathplot.R (line 203, column 21)
R/bnpathplot.R (line 224, column 34)
R/bnpathplot.R (line 342, column 21)
R/bnpathplot.R (line 343, column 30)
R/bnpathplot.R (line 344, column 31)
R/bnpathplot.R (line 351, column 21)
R/bnpathplot.R (line 352, column 30)
R/bnpathplot.R (line 353, column 31)
R/bnpathplot.R (line 371, column 29)
R/bnpathplot.R (line 373, column 29)
R/bnpathplot.R (line 375, column 29)
R/bnpathplotCustom.R (line 74, column 39)
R/bnpathplotCustom.R (line 83, column 23)
R/bnpathplotCustom.R (line 85, column 23)
R/bnpathplotCustom.R (line 101, column 31)
R/bnpathplotCustom.R (line 118, column 13)
R/bnpathplotCustom.R (line 123, column 21)
R/bnpathplotCustom.R (line 147, column 34)
R/bnpathplotCustom.R (line 268, column 17)
R/bnpathplotCustom.R (line 269, column 26)
R/bnpathplotCustom.R (line 270, column 27)
R/bnpathplotCustom.R (line 273, column 17)
R/bnpathplotCustom.R (line 274, column 26)
R/bnpathplotCustom.R (line 275, column 27)
R/utilities.R (line 192, column 9)
R/utilities.R (line 229, column 39)
R/utilities.R (line 321, column 39)
R/utilities.R (line 425, column 12)
R/utilities.R (line 426, column 10)
R/utilities.R (line 427, column 13)
R/utilities.R (line 428, column 13)
R/utilities.R (line 430, column 17)
R/utilities.R (line 432, column 15)
R/utilities.R (line 433, column 11)
R/utilities.R (line 436, column 23)
R/utilities.R (line 438, column 23)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
suppressMessages() in R/bnpathplot.R (line 206, column 27)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 7 functions > 50 lines.
The longest 5 functions are:
bngeneplot() (R/bngeneplot.R, line 63): 463 lines
bnpathplot() (R/bnpathplot.R, line 64): 395 lines
bnpathplotCustom() (R/bnpathplotCustom.R, line 61): 320 lines
bngeneplotCustom() (R/bngeneplotCustom.R, line 62): 298 lines
bnpathtest() (R/utilities.R, line 226): 63 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
queryCpDistLs.Rd, queryCpDistLw.Rd
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
15% of man pages use one of these cases.
Found in the following files:
queryCpDistLs.Rd
queryCpDistLw.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
queryCpDistLs.Rd
queryCpDistLw.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; 355 lines (11%) are > 80 characters
long.
First 6 lines:
R/bngeneplot.R:5 #' @param results the enrichment analysis result from ...
R/bngeneplot.R:8 #' @param expSample candidate samples to be included i...
R/bngeneplot.R:9 #' @param algo structure learning method used in boot....
R/bngeneplot.R:10 #' @param algorithm.args parameters to pass to bnlear...
R/bngeneplot.R:12 #' @param pathNum the pathway number (the number of r...
R/bngeneplot.R:13 #' @param convertSymbol whether the label of resultin...
* NOTE: Consider multiples of 4 spaces for line indents, 398
lines(12%) are not.
First 6 lines:
R/bngeneplot.R:109 axis.text = element_text(size=10),
R/bngeneplot.R:110 axis.title = element_text(size=12))
R/bngeneplot.R:132 # rn <- clusterProfiler::bitr(rownames(pcs),
R/bngeneplot.R:133 # fromType=exp...
R/bngeneplot.R:134 # toType="SYMB...
R/bngeneplot.R:135 # OrgDb=org.Hs...
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...
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 10
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
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir CBNplot_0.99.2.tar.gz'
>>>>>>>
* installing *source* package ‘CBNplot’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CBNplot)