Altuna Akalin
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_12 |
| Last Commit: a48c559 |
| Last Changed Date: 2021-01-28 09:43:19 -0400 (Thu, 28 Jan 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:35:41 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the methylKit package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1077/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylKit 1.16.1 (landing page) Altuna Akalin
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: methylKit |
| Version: 1.16.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylKit_1.16.1.tar.gz |
| StartedAt: 2021-05-06 03:36:31 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:44:26 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 475.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylKit.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylKit_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/methylKit.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methylKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylKit’ version ‘1.16.1’
* 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
* 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 ... 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 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 ... 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 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methylKit/libs/methylKit.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (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 ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘_srand48’, possibly from ‘srand48’ (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. 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 12.139 0.284 12.455
selectByOverlap-methods 5.284 0.094 5.398
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/methylKit.Rcheck/00check.log’
for details.
methylKit.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylKit
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c methCall.cpp -o methCall.o
In file included from methCall.cpp:18:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o methylKit.so RcppExports.o methCall.o /Library/Frameworks/R.framework/Versions/4.0/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/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
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 234 ]
>
> proc.time()
user system elapsed
114.235 2.127 116.719
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.047 | 0.006 | 0.054 | |
| adjustMethylC | 0.175 | 0.010 | 0.187 | |
| assocComp-methods | 0.065 | 0.004 | 0.070 | |
| bedgraph-methods | 0.040 | 0.006 | 0.046 | |
| calculateDiffMeth-methods | 12.139 | 0.284 | 12.455 | |
| calculateDiffMethDSS-methods | 0.965 | 0.009 | 0.977 | |
| clusterSamples-methods | 0.065 | 0.004 | 0.069 | |
| dataSim-methods | 0.030 | 0.003 | 0.033 | |
| diffMethPerChr-methods | 0.063 | 0.004 | 0.068 | |
| extract-methods | 0.046 | 0.003 | 0.050 | |
| filterByCoverage-methods | 0.152 | 0.008 | 0.160 | |
| getAssembly-methods | 0.018 | 0.003 | 0.021 | |
| getContext-methods | 0.018 | 0.003 | 0.021 | |
| getCorrelation-methods | 0.094 | 0.008 | 0.102 | |
| getCoverageStats-methods | 0.024 | 0.003 | 0.028 | |
| getDBPath-methods | 0.080 | 0.008 | 0.088 | |
| getData-methods | 0.028 | 0.004 | 0.032 | |
| getMethylDiff-methods | 0.027 | 0.002 | 0.030 | |
| getMethylationStats-methods | 0.035 | 0.003 | 0.038 | |
| getSampleID-methods | 0.018 | 0.003 | 0.021 | |
| getTreatment-methods | 0.019 | 0.003 | 0.022 | |
| makeMethylDB-methods | 0.001 | 0.000 | 0.001 | |
| methRead-methods | 0.373 | 0.031 | 0.407 | |
| methSeg | 0.001 | 0.000 | 0.001 | |
| methylBase-class | 0.036 | 0.002 | 0.038 | |
| methylBaseDB-class | 0.123 | 0.008 | 0.131 | |
| methylDiff-class | 0.043 | 0.002 | 0.046 | |
| methylDiffDB-class | 4.359 | 0.017 | 4.390 | |
| methylRaw-class | 0.102 | 0.007 | 0.108 | |
| methylRawDB-class | 0.127 | 0.009 | 0.136 | |
| methylRawList-class | 0.018 | 0.002 | 0.020 | |
| methylRawListDB-class | 0.205 | 0.020 | 0.225 | |
| normalizeCoverage-methods | 0.202 | 0.016 | 0.218 | |
| percMethylation-methods | 0.044 | 0.003 | 0.047 | |
| pool-methods | 0.027 | 0.002 | 0.029 | |
| processBismarkAln-methods | 0.087 | 0.011 | 0.100 | |
| readMethylDB-methods | 0.001 | 0.000 | 0.001 | |
| reconstruct-methods | 0.037 | 0.003 | 0.039 | |
| regionCounts | 0.624 | 0.005 | 0.637 | |
| removeComp-methods | 0.055 | 0.004 | 0.059 | |
| reorganize-methods | 0.216 | 0.006 | 0.223 | |
| select-methods | 0.137 | 0.013 | 0.151 | |
| selectByOverlap-methods | 5.284 | 0.094 | 5.398 | |
| show-methods | 0.048 | 0.005 | 0.052 | |
| tileMethylCounts-methods | 1.058 | 0.010 | 1.073 | |
| unite-methods | 0.196 | 0.007 | 0.205 | |