Tom Mayo
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/M3D |
| Branch: RELEASE_3_11 |
| Last Commit: 09ed714 |
| Last Changed Date: 2020-04-27 14:42:10 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:59 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE M3D PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 965/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Tom Mayo
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: M3D |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:M3D.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings M3D_1.22.0.tar.gz |
| StartedAt: 2020-10-17 05:34:36 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:39:23 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 286.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: M3D.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:M3D.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings M3D_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'M3D/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'M3D' version '1.22.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'M3D' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck/00install.out' for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
M3D_Wrapper: no visible global function definition for 'txtProgressBar'
M3D_Wrapper: no visible global function definition for
'setTxtProgressBar'
M3D_Wrapper_lite: no visible global function definition for
'txtProgressBar'
M3D_Wrapper_lite: no visible global function definition for
'setTxtProgressBar'
plotCoverageSampleProfiles: no visible global function definition for
'lines'
plotCoverageSampleProfiles: no visible global function definition for
'points'
plotCoverageSampleProfiles: no visible global function definition for
'title'
plotMethProfile: no visible global function definition for 'lines'
plotMethProfile: no visible global function definition for 'points'
plotMethProfile: no visible global function definition for 'title'
plotMethSampleProfiles: no visible global function definition for
'lines'
plotMethSampleProfiles: no visible global function definition for
'points'
plotMethSampleProfiles: no visible global function definition for
'title'
pvals: no visible global function definition for 'p.adjust'
pvals_lite: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
lines p.adjust points setTxtProgressBar title txtProgressBar
Consider adding
importFrom("graphics", "lines", "points", "title")
importFrom("stats", "p.adjust")
importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/M3D/libs/x64/M3D.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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
* 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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/M3D.Rcheck/00check.log'
for details.
M3D.Rcheck/00install.out
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch M3D
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* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
* installing *source* package 'M3D' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp_fns.cpp -o cpp_fns.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o M3D.dll tmp.def RcppExports.o cpp_fns.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.11-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/R/library/00LOCK-M3D/00new/M3D/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'M3D'
finding HTML links ... done
CpGsDemo html
M3D-package html
M3D_Single html
M3D_Wrapper html
M3D_Wrapper_lite html
MMDlistDemo html
PDemo html
determineGroupComps html
findComps html
medianFreq html
median_freq html
plotCoverageSampleProfiles html
plotMethProfile html
plotMethSampleProfiles html
pvals html
pvals_lite html
readBedFiles html
readBedRaw html
rrbsDemo html
test_colData_structure html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'M3D' is deprecated and will be removed from Bioconductor
version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (M3D)
Making 'packages.html' ... done
M3D.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(M3D)
Warning message:
Package 'M3D' is deprecated and will be removed from Bioconductor
version 3.12
>
> test_check("M3D")
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== testthat results ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.40 0.68 17.09
M3D.Rcheck/M3D-Ex.timings
| name | user | system | elapsed | |
| M3D_Wrapper | 1.38 | 0.02 | 1.39 | |
| M3D_Wrapper_lite | 0.22 | 0.00 | 0.22 | |
| determineGroupComps | 0.45 | 0.03 | 0.49 | |
| findComps | 0.36 | 0.05 | 0.40 | |
| median_freq | 0 | 0 | 0 | |
| plotCoverageSampleProfiles | 0.35 | 0.00 | 0.34 | |
| plotMethProfile | 0.25 | 0.00 | 0.25 | |
| plotMethSampleProfiles | 0.23 | 0.01 | 0.25 | |
| pvals | 0.63 | 0.05 | 0.67 | |
| pvals_lite | 0.44 | 0.00 | 0.44 | |
| readBedFiles | 0 | 0 | 0 | |
| readBedRaw | 0 | 0 | 0 | |