Altuna Akalin
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 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 2023-10-16 11:35:31 -0400 (Mon, 16 Oct 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" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings methylKit_1.26.0.tar.gz |
| StartedAt: 2023-10-15 22:42:58 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 22:49:02 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 363.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methylKit.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings methylKit_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/methylKit.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
R 1.0Mb
libs 3.1Mb
* 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/methylKit/libs/methylKit.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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 5.382 0.207 5.59
* 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 ...
‘methylKit.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/methylKit.Rcheck/00check.log’
for details.
methylKit.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL methylKit
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c methCall.cpp -o methCall.o
methCall.cpp: In function ‘int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int, size_t&)’:
methCall.cpp:687:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
687 | if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:686:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
686 | if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:685:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
685 | if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int, size_t&)’:
methCall.cpp:1014:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1014 | if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1013:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1013 | if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1012:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1012 | if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function ‘int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, size_t&)’:
methCall.cpp:1244:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1244 | if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1243:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1243 | if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1242:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1242 | if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /home/biocbuild/bbs-3.17-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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-pc-linux-gnu (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
68.076 1.751 68.612
methylKit.Rcheck/methylKit-Ex.timings
| name | user | system | elapsed | |
| PCASamples-methods | 0.021 | 0.003 | 0.025 | |
| adjustMethylC | 0.168 | 0.004 | 0.160 | |
| assocComp-methods | 0.018 | 0.000 | 0.018 | |
| bedgraph-methods | 0.025 | 0.000 | 0.025 | |
| calculateDiffMeth-methods | 5.382 | 0.207 | 5.590 | |
| calculateDiffMethDSS-methods | 0.383 | 0.008 | 0.391 | |
| clusterSamples-methods | 0.026 | 0.004 | 0.030 | |
| dataSim-methods | 0.016 | 0.000 | 0.016 | |
| diffMethPerChr-methods | 0.032 | 0.001 | 0.026 | |
| extract-methods | 0.017 | 0.008 | 0.024 | |
| filterByCoverage-methods | 0.052 | 0.003 | 0.056 | |
| getAssembly-methods | 0.009 | 0.001 | 0.008 | |
| getContext-methods | 0.008 | 0.000 | 0.008 | |
| getCorrelation-methods | 0.066 | 0.007 | 0.057 | |
| getCoverageStats-methods | 0.012 | 0.000 | 0.013 | |
| getDBPath-methods | 0.051 | 0.008 | 0.044 | |
| getData-methods | 0.008 | 0.008 | 0.016 | |
| getMethylDiff-methods | 0.006 | 0.007 | 0.014 | |
| getMethylationStats-methods | 0.014 | 0.004 | 0.018 | |
| getSampleID-methods | 0.009 | 0.000 | 0.009 | |
| getTreatment-methods | 0.009 | 0.001 | 0.009 | |
| makeMethylDB-methods | 0 | 0 | 0 | |
| methRead-methods | 0.225 | 0.015 | 0.241 | |
| methSeg | 0 | 0 | 0 | |
| methylBase-class | 0.014 | 0.004 | 0.019 | |
| methylBaseDB-class | 0.072 | 0.001 | 0.058 | |
| methylDiff-class | 0.021 | 0.000 | 0.021 | |
| methylDiffDB-class | 1.605 | 0.000 | 1.604 | |
| methylRaw-class | 0.053 | 0.000 | 0.053 | |
| methylRawDB-class | 0.082 | 0.000 | 0.072 | |
| methylRawList-class | 0.009 | 0.000 | 0.009 | |
| methylRawListDB-class | 0.114 | 0.016 | 0.130 | |
| normalizeCoverage-methods | 0.121 | 0.000 | 0.121 | |
| percMethylation-methods | 0.015 | 0.004 | 0.020 | |
| pool-methods | 0.005 | 0.008 | 0.013 | |
| processBismarkAln-methods | 0.037 | 0.004 | 0.042 | |
| readMethylDB-methods | 0 | 0 | 0 | |
| reconstruct-methods | 0.013 | 0.003 | 0.015 | |
| regionCounts | 0.266 | 0.000 | 0.267 | |
| removeComp-methods | 0.023 | 0.000 | 0.024 | |
| reorganize-methods | 0.150 | 0.000 | 0.103 | |
| select-methods | 0.077 | 0.012 | 0.073 | |
| selectByOverlap-methods | 2.094 | 0.036 | 2.099 | |
| show-methods | 0.024 | 0.000 | 0.025 | |
| tileMethylCounts-methods | 0.422 | 0.004 | 0.403 | |
| unite-methods | 0.154 | 0.008 | 0.099 | |