===============================
BiocCheckGitClone('IntOMICS')
===============================
─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2744/a4b0fad3eb2ed5e4c9b71d51991fac2b11ced26b/IntOMICS
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2744/a4b0fad3eb2ed5e4c9b71d51991fac2b11ced26b/IntOMICS.Rcheck’
* using R Under development (unstable) (2022-10-25 r83175)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IntOMICS’ version ‘0.99.5’
* 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 ‘IntOMICS’ 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 ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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
dens_edge_weights: no visible binding for global variable ‘edge_weight’
dens_edge_weights: no visible binding for global variable ‘scaled’
ggraph_weighted_net: no visible binding for global variable
‘weighted_net_res’
ggraph_weighted_net: no visible binding for global variable
‘node2.degree’
ggraph_weighted_net: no visible binding for global variable ‘weight’
ggraph_weighted_net: no visible binding for global variable ‘color’
ggraph_weighted_net: no visible binding for global variable ‘label’
legend_custom_ggplot: no visible binding for global variable ‘x_min’
legend_custom_ggplot: no visible binding for global variable ‘x_max’
legend_custom_ggplot: no visible binding for global variable ‘y_min’
legend_custom_ggplot: no visible binding for global variable ‘y_max’
legend_custom_ggplot: no visible binding for global variable ‘x_lab’
legend_custom_ggplot: no visible binding for global variable ‘val’
Undefined global functions or variables:
color edge_weight label node2.degree scaled val weight
weighted_net_res x_lab x_max x_min y_max y_min
* 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 ... [12s/12s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] ERROR
Running examples in ‘IntOMICS-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: init_net_mcmc
> ### Title: Random initial network
> ### Aliases: init_net_mcmc
> ### Keywords: internal
>
> ### ** Examples
>
> data(list=c("PK", "TFtarg_mat", "annot", "layers_def", "omics",
+ "gene_annot"), package="IntOMICS")
> omics <- omics_to_list(omics = omics, layers_def = layers_def,
+ gene_annot = gene_annot)
Loading required package: MultiAssayExperiment
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, aperm, 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: HDF5Array
Loading required package: DelayedArray
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:base’:
apply, rowsum, scale, sweep
Loading required package: rhdf5
Attaching package: ‘HDF5Array’
The following object is masked from ‘package:rhdf5’:
h5ls
Error in file_path_as_absolute(filepath) :
file '/home/annapacinkova/.cache/R/ExperimentHub/4a8d7c2fdea_4873' does not exist
Calls: omics_to_list ... .h5openfile -> .h5openlocalfile -> file_path_as_absolute
Execution halted
* checking for unstated dependencies in ‘tests’ ... WARNING
'library' or 'require' call not declared from: ‘testthat’
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('IntOMICS_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.35.4
─ BiocVersion: 3.17
─ Package: IntOMICS
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpeLyFH4/file2af56a87e1558/IntOMICS
─ installDir: /tmp/RtmpeLyFH4/file2af56a7d869b5e
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2744/a4b0fad3eb2ed5e4c9b71d51991fac2b11ced26b/IntOMICS.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 4.2.0 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...
* 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...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import grid in DESCRIPTION as well as NAMESPACE.
* 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 IntOMICS...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
Found @ in man/dens_edge_weights.Rd
Found @ in man/ggraph_weighted_net.Rd
Found @ in man/legend_custom_ggplot.Rd
Found @ in man/weighted_net.Rd
Found @ in vignettes/IntOMICS_vignette.Rmd
* NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 132 functions greater than 50 lines.
* Checking man page documentation...
* ERROR: At least 80% of man pages documenting exported objects
must have runnable examples.
* 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; 90 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 794 lines
(11%) 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...
* NOTE: Cannot determine whether maintainer is subscribed to the
Bioc-Devel mailing list (requires admin credentials). Subscribe
here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
1 ERRORS | 1 WARNINGS | 8 NOTES
See the IntOMICS.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.