===============================
BiocCheckGitClone('STdeconvolve')
===============================
This is BiocCheckGitClone version 1.31.36. 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
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R CMD CHECK
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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2530/6dac0f273f761bce8d890c05a86809b05d5e19eb/STdeconvolve.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STdeconvolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STdeconvolve’ version ‘0.99.7’
* 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 ‘STdeconvolve’ can be installed ... [6s/6s] 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 ... [7s/7s] NOTE
correlationPlot: no visible binding for global variable ‘Var1’
correlationPlot: no visible binding for global variable ‘Var2’
correlationPlot: no visible binding for global variable ‘value’
fitLDA: no visible binding for global variable ‘rareCtsAdj’
fitLDA: no visible binding for global variable ‘K’
fitLDA: no visible binding for global variable ‘perplexAdj’
fitLDA: no visible binding for global variable ‘alphaBool’
perplexityPlot: no visible binding for global variable ‘rareCtsAdj’
perplexityPlot: no visible binding for global variable ‘K’
perplexityPlot: no visible binding for global variable ‘perplexAdj’
perplexityPlot: no visible binding for global variable ‘alphaBool’
vizAllTopics: no visible binding for global variable ‘x’
vizAllTopics: no visible binding for global variable ‘y’
vizAllTopics: no visible binding for global variable ‘Row.names’
vizAllTopics: no visible binding for global variable ‘Pixel.Groups’
vizGeneCounts: no visible binding for global variable ‘x’
vizGeneCounts: no visible binding for global variable ‘y’
vizTopic: no visible binding for global variable ‘x’
vizTopic: no visible binding for global variable ‘y’
Undefined global functions or variables:
K Pixel.Groups Row.names Var1 Var2 alphaBool perplexAdj rareCtsAdj
value x y
* 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 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 ... [145s/273s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
perplexityPlot 28.424 0.066 28.492
vizAllTopics 20.996 0.234 21.232
correlationPlot 19.400 0.174 19.576
vizTopic 17.852 0.086 17.941
lsatPairs 17.514 0.067 17.583
getCorrMtx 17.508 0.056 17.564
fitLDA 2.718 0.153 29.195
getBetaTheta 2.557 0.118 28.868
topGenes 2.394 0.116 28.906
optimalModel 2.385 0.090 50.587
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [102s/102s]
[102s/102s] 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: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2530/6dac0f273f761bce8d890c05a86809b05d5e19eb/STdeconvolve.Rcheck/00check.log’
for details.
===============================
BiocCheck('STdeconvolve_0.99.7.tar.gz')
===============================
This is BiocCheck version 1.31.36. 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/2530/6dac0f273f761bce8d890c05a86809b05d5e19eb/STdeconvolve_0.99.7.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpZycJ6l/file1176f6adfd9de/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...
* NOTE: Update R version dependency from 3.6 to 4.2.0.
* 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...
* 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...
* ERROR: More than one VignetteEngine specified.
Found in vignette/ files:
vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of STdeconvolve...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/functions.R (line 518, column 37)
R/functions.R (line 721, column 7)
R/functions.R (line 758, column 7)
R/functions.R (line 858, column 31)
R/functions.R (line 860, column 31)
R/functions.R (line 862, column 31)
R/functions.R (line 863, column 23)
R/functions.R (line 864, column 31)
R/import.R (line 19, column 24)
R/plot.R (line 506, column 26)
R/plot.R (line 520, column 37)
* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
functions.R (line 82, column 57)
functions.R (line 242, column 83)
functions.R (line 323, column 59)
functions.R (line 493, column 17)
functions.R (line 733, column 37)
functions.R (line 734, column 14)
functions.R (line 760, column 37)
functions.R (line 771, column 14)
functions.R (line 1006, column 38)
import.R (line 224, column 25)
plot.R (line 519, column 17)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/functions.R (line 766, column 21)
print() in R/functions.R (line 344, column 3)
print() in R/functions.R (line 574, column 5)
print() in R/plot.R (line 572, column 3)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/import.R (line 151, column 35)
* NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/functions.R (line 39, column 13)
R/functions.R (line 44, column 13)
R/functions.R (line 50, column 13)
R/functions.R (line 55, column 13)
R/functions.R (line 60, column 13)
R/import.R (line 163, column 15)
R/import.R (line 182, column 13)
R/import.R (line 310, column 13)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/functions.R (line 272, column 15)
R/functions.R (line 292, column 15)
R/functions.R (line 779, column 25)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 10 functions > 50 lines.
The longest 5 functions are:
preprocess() (R/functions.R, line 165): 203 lines
fitLDA() (R/functions.R, line 409): 178 lines
vizAllTopics() (R/plot.R, line 45): 113 lines
getOverdispersedGenes() (R/import.R, line 122): 88 lines
getCorrMtx() (R/functions.R, line 692): 87 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
annotateCellTypesGSEA.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 274 lines (8%) are > 80 characters
long.
First 6 lines:
R/data.R:3 #' @format List where 'counts' is a sparse matrix with colum...
R/data.R:13 # @format List where 'mat' is a sparse matrix with columns ...
R/data.R:14 # where expression values have alr...
R/data.R:16 # and brain position as 6 slice in...
R/data.R:23 #' @format List where 'counts' is a sparse matrix with colu...
R/functions.R:3 #' @description identifies over dispersed genes across ...
* NOTE: Consider multiples of 4 spaces for line indents, 1015
lines(30%) are not.
First 6 lines:
R/functions.R:29 removeAbove=1.0,
R/functions.R:30 removeBelow=0.05,
R/functions.R:31 alpha=0.05,
R/functions.R:32 nTopOD=1000,
R/functions.R:33 plot=FALSE,
R/functions.R:34 verbose=TRUE) {
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: 1
WARNING count: 0
NOTE count: 11
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.