Altuna Akalin
| Snapshot Date: 2023-09-24 14:00:11 -0400 (Sun, 24 Sep 2023) |
| git_url: https://git.bioconductor.org/packages/methylKit |
| git_branch: RELEASE_3_17 |
| git_last_commit: a15614f |
| git_last_commit_date: 2023-04-25 10:48:14 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-09-25 11:37:23 -0400 (Mon, 25 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1200/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylKit 1.26.0 (landing page) Altuna Akalin
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the methylKit package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylKit.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: methylKit |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylKit_1.26.0.tar.gz |
| StartedAt: 2023-09-25 04:16:21 -0400 (Mon, 25 Sep 2023) |
| EndedAt: 2023-09-25 04:31:46 -0400 (Mon, 25 Sep 2023) |
| EllapsedTime: 924.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methylKit.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylKit_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/methylKit.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylKit’ version ‘1.26.0’
* 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 ‘methylKit’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
is used with destrand=TRUE argument. It returned less number of CpGs then it was
Cannot process chunk/lines:
supposed to, although returned CpGs had correct methylation and coverage values.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘KernSmooth’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'methylRawList-class'
‘...’ ‘treatment’
Undocumented arguments in documentation object 'methylRawListDB-class'
‘...’ ‘treatment’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/methylKit/libs/methylKit.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_exit’, possibly from ‘exit’ (C)
Found ‘_sprintf’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculateDiffMeth-methods 14.115 0.489 19.448
selectByOverlap-methods 5.759 0.146 8.466
methylDiffDB-class 4.633 0.034 6.480
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/methylKit.Rcheck/00check.log’
for details.
methylKit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylKit ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘methylKit’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methCall.cpp -o methCall.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o methylKit.so RcppExports.o methCall.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-methylKit/00new/methylKit/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (methylKit)
methylKit.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(methylKit)
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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
>
>
> test_check("methylKit")
Using internal DSS code...
Using internal DSS code...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 238 ]
>
> proc.time()
user system elapsed
169.647 3.893 232.734
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.170 | 0.011 | 0.247 | |
| adjustMethylC | 0.129 | 0.010 | 0.314 | |
| assocComp-methods | 0.034 | 0.005 | 0.040 | |
| bedgraph-methods | 0.042 | 0.010 | 0.326 | |
| calculateDiffMeth-methods | 14.115 | 0.489 | 19.448 | |
| calculateDiffMethDSS-methods | 1.020 | 0.015 | 1.318 | |
| clusterSamples-methods | 0.066 | 0.006 | 0.092 | |
| dataSim-methods | 0.029 | 0.005 | 0.039 | |
| diffMethPerChr-methods | 0.051 | 0.005 | 0.067 | |
| extract-methods | 0.047 | 0.005 | 0.064 | |
| filterByCoverage-methods | 0.105 | 0.011 | 0.150 | |
| getAssembly-methods | 0.016 | 0.004 | 0.022 | |
| getContext-methods | 0.017 | 0.004 | 0.030 | |
| getCorrelation-methods | 0.100 | 0.012 | 0.149 | |
| getCoverageStats-methods | 0.022 | 0.005 | 0.032 | |
| getDBPath-methods | 0.079 | 0.009 | 0.110 | |
| getData-methods | 0.033 | 0.007 | 0.051 | |
| getMethylDiff-methods | 0.030 | 0.004 | 0.043 | |
| getMethylationStats-methods | 0.035 | 0.006 | 0.051 | |
| getSampleID-methods | 0.017 | 0.004 | 0.025 | |
| getTreatment-methods | 0.016 | 0.004 | 0.028 | |
| makeMethylDB-methods | 0.001 | 0.001 | 0.001 | |
| methRead-methods | 0.407 | 0.040 | 0.569 | |
| methSeg | 0.000 | 0.000 | 0.001 | |
| methylBase-class | 0.039 | 0.004 | 0.052 | |
| methylBaseDB-class | 0.110 | 0.009 | 0.145 | |
| methylDiff-class | 0.044 | 0.003 | 0.061 | |
| methylDiffDB-class | 4.633 | 0.034 | 6.480 | |
| methylRaw-class | 0.106 | 0.014 | 0.180 | |
| methylRawDB-class | 0.149 | 0.016 | 0.233 | |
| methylRawList-class | 0.017 | 0.004 | 0.022 | |
| methylRawListDB-class | 0.214 | 0.030 | 0.413 | |
| normalizeCoverage-methods | 0.204 | 0.023 | 0.340 | |
| percMethylation-methods | 0.044 | 0.005 | 0.069 | |
| pool-methods | 0.026 | 0.004 | 0.041 | |
| processBismarkAln-methods | 0.087 | 0.021 | 0.204 | |
| readMethylDB-methods | 0.000 | 0.001 | 0.006 | |
| reconstruct-methods | 0.034 | 0.004 | 0.049 | |
| regionCounts | 0.656 | 0.012 | 0.996 | |
| removeComp-methods | 0.053 | 0.004 | 0.084 | |
| reorganize-methods | 0.226 | 0.012 | 0.363 | |
| select-methods | 0.145 | 0.020 | 0.324 | |
| selectByOverlap-methods | 5.759 | 0.146 | 8.466 | |
| show-methods | 0.045 | 0.008 | 0.073 | |
| tileMethylCounts-methods | 1.007 | 0.019 | 1.408 | |
| unite-methods | 0.203 | 0.007 | 0.263 | |