===============================
R CMD BUILD
===============================
* checking for file ‘APL/DESCRIPTION’ ... OK
* preparing ‘APL’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘APL.Rmd’ using rmarkdown
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: scuttle
Loading required package: ggplot2
Quitting from lines 167-173 (APL.Rmd)
Error: processing vignette 'APL.Rmd' failed with diagnostics:
ModuleNotFoundError: No module named 'torch'
Detailed traceback:
File "<string>", line 3, in <module>
File "/home/biocbuild/bbs-3.15-bioc/R/library/reticulate/python/rpytools/loader.py", line 39, in _import_hook
module = _import(
--- failed re-building ‘APL.Rmd’
SUMMARY: processing the following file failed:
‘APL.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
BiocCheckGitClone('APL')
===============================
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...
* Checking that provided CITATION file is correctly formatted...
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/2465/ba22831892ba3695727621db901d75cdc727f91c/APL.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 ‘APL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘APL’ version ‘0.99.4’
* 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 ‘APL’ can be installed ... [78s/80s] 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 ... [76s/80s] OK
* checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [73s/78s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
apl_topGO 10.382 0.31 11.626
plot_enrichment 9.730 0.15 9.934
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [26s/26s]
[26s/27s] 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: OK
===============================
BiocCheck('APL_0.99.4.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/2465/ba22831892ba3695727621db901d75cdc727f91c/APL_0.99.4.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpjliK8S/file9412181737c3/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...
* 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...
* NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict 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 APL...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/generic_methods.R (line 24, column 5)
cat() in R/generic_methods.R (line 32, column 5)
cat() in R/generic_methods.R (line 35, column 3)
cat() in R/generic_methods.R (line 42, column 3)
cat() in R/generic_methods.R (line 49, column 3)
cat() in R/generic_methods.R (line 58, column 5)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/apl.R (line 985, column 25)
R/apl.R (line 1203, column 25)
R/apl.R (line 1294, column 25)
R/CA.R (line 330, column 25)
R/CA.R (line 402, column 25)
R/CA.R (line 495, column 25)
R/CA.R (line 943, column 25)
R/CA.R (line 1031, column 25)
R/CA.R (line 1094, column 25)
R/convert.R (line 238, column 42)
R/convert.R (line 269, column 25)
R/convert.R (line 306, column 25)
R/convert.R (line 354, column 25)
R/plot.R (line 58, column 25)
R/plot.R (line 154, column 25)
R/plot.R (line 185, column 25)
R/plot.R (line 275, column 25)
R/plot.R (line 424, column 25)
R/plot.R (line 455, column 25)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
suppressWarnings() in R/apl.R (line 217, column 7)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 17 functions > 50 lines.
The longest 5 functions are:
check_cacomp() (R/constructor.R, line 24): 226 lines
recompute() (R/convert.R, line 20): 187 lines
_anonymous_.986() (R/apl.R, line 986): 180 lines
apl_plotly() (R/apl.R, line 551): 153 lines
_anonymous_.276() (R/plot.R, line 276): 143 lines
* Checking man page documentation...
* 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; 113 lines (2%) are > 80 characters
long.
First 6 lines:
R/apl.R:1111 stopifnot("Cannot use scree plot to pick dimensions"...
R/apl.R:1172 message("\nBoth dims and pd_use set. Using dimen...
R/CA.R:225 reticulate::source_python(system.file("python/python_svd...
R/CA.R:464 stopifnot("Set coords = TRUE when inputting a Seurat objec...
R/CA.R:484 obj[["CA"]] <- Seurat::CreateDimReducObject(embeddings =...
R/CA.R:485 loadings = ca...
* NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain
tabs.
First 3 lines:
R/CA.R:109 chisquare <- res$tot * (res$S^2) # chi-square components ...
R/CA.R:943 dim_number <- max_num_dims
R/CA.R:949 dim_number <- length(tmp[cumsum(tmp == 0)<1 & tmp!=0])
* NOTE: Consider multiples of 4 spaces for line indents, 1977
lines(28%) are not.
First 6 lines:
R/apl.R:55 stopifnot(is(caobj, "cacomp"))
R/apl.R:57 rows <- caobj@prin_coords_rows
R/apl.R:58 cols <- caobj@std_coords_cols
R/apl.R:59 cent <- cols
R/apl.R:62 if (is(group, "numeric")){
R/apl.R:64 } else if (is(group, "character")){
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: 8
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