===============================
R CMD BUILD
===============================
* checking for file ‘mariner/DESCRIPTION’ ... OK
* preparing ‘mariner’:
* 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
* building ‘mariner_0.99.1.tar.gz’
===============================
BiocCheckGitClone('mariner')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: mariner
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3002/mariner_20230411120332/mariner
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* ERROR: System files found that should not be Git tracked.
mariner.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc 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 ──
1 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3002/mariner_20230411120332/mariner.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mariner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mariner’ version ‘0.99.1’
* 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 ‘mariner’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 17.2Mb
sub-directories of 1Mb or more:
extdata 16.0Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘plotgardener:::check_page’ ‘plotgardener:::convert_page’
‘plotgardener:::current_viewports’ ‘plotgardener:::defaultUnits’
‘plotgardener:::pgEnv’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [45s/45s] OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] ERROR
Running examples in ‘mariner-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CountMatrix-class
> ### Title: CountMatrix Class
> ### Aliases: CountMatrix-class CountMatrix show,CountMatrix-method
> ### Keywords: internal
>
> ### ** Examples
>
> ## Read .hic file paths
> hicFiles <-
+ system.file("extdata/test_hic", package="mariner") |>
+ list.files(pattern=".hic", full.names=TRUE)
>
> ## Read in loop pixels as GInteractions object
> pixels <-
+ system.file("extdata", package="mariner") |>
+ list.files(pattern="WT.*Loops.txt", full.names=TRUE) |>
+ read.table(header=TRUE) |>
+ as_ginteractions(keep.extra.columns=FALSE) |>
+ binPairs(binSize=100e3)
>
> ## Removes the "chr" prefix for compatibility
> ## with the preprocessed hic files
> GenomeInfoDb::seqlevelsStyle(pixels) <- 'ENSEMBL'
>
> ## Expand pixels to regions for pulling
> ## Hi-C submatrices
> regions <- pixelsToMatrices(x=pixels, buffer=5)
>
> ## Extract 11x11 count matrices from the
> ## first 100 regions and 2 Hi-C files
> iarr <- pullHicMatrices(x=regions[1:100],
+ files=hicFiles,
+ binSize=100e3)
Error in chrMaps[[1]] : subscript out of bounds
Calls: pullHicMatrices ... pullHicMatrices -> .local -> .prepareInputs -> .checkHicChroms
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [209s/111s]
[209s/112s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
── Error ('test_pullHic.R:618:5'): Error when trying to pull irregular arrays ──
<Rcpp::exception/C++Error/error/condition>
Error: File NA cannot be opened for reading.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_pullHic.R:618:4
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─mariner::pullHicMatrices(gi, hicFiles[1], 1e+05, half = "both")
8. └─mariner::pullHicMatrices(gi, hicFiles[1], 1e+05, half = "both")
9. └─mariner (local) .local(...)
10. └─mariner:::.prepareInputs(...)
11. └─mariner:::.checkStrawArgs(files, half, norm, binSize, matrix)
12. ├─rlang::arg_match(norm, readHicNormTypes(f))
13. └─strawr::readHicNormTypes(f)
[ FAIL 25 | WARN 0 | SKIP 1 | PASS 351 ]
Error: Test failures
Execution halted
* 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 ... [3s/3s] OK
* DONE
Status: 2 ERRORs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3002/mariner_20230411120332/mariner.Rcheck/00check.log’
for details.
===============================
BiocCheck('mariner_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.18
─ BiocVersion: 3.17
─ Package: mariner
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpT5Wymq/file29769e179a9a7a/mariner
─ installDir: /tmp/RtmpT5Wymq/file29769e6ba69337
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3002/mariner_20230411120332/mariner.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...
* ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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 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 mariner...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 12 functions greater than 50 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; 20 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 759 lines
(7%) 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...
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.
─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 5 NOTES
See the mariner.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.