Tom Mayo
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/M3D |
| Branch: RELEASE_3_6 |
| Last Commit: be02c7b |
| Last Changed Date: 2017-10-30 12:40:21 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:06 -0400 (Thu, 12 Apr 2018).
| Package 767/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| M3D 1.12.0 Tom Mayo
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: M3D |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings M3D_1.12.0.tar.gz |
| StartedAt: 2018-04-12 05:42:54 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 05:47:05 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 250.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: M3D.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings M3D_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3D/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘M3D’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘M3D’ 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 loading without being on the library search path ... 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
‘plot’
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 ‘plot’
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
‘plot’
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 plot points setTxtProgressBar title txtProgressBar
Consider adding
importFrom("graphics", "lines", "plot", "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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/00check.log’
for details.
M3D.Rcheck/00install.out
* installing *source* package ‘M3D’ ... ** libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_fns.cpp -o cpp_fns.o clang++ -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 M3D.so RcppExports.o cpp_fns.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.6-bioc/meat/M3D.Rcheck/M3D/libs ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (M3D)
M3D.Rcheck/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.
> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(M3D)
>
> test_check("M3D")
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══ testthat results ═══════════════════════════════════════════════════════════
OK: 20 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.175 0.480 12.949
M3D.Rcheck/M3D-Ex.timings
| name | user | system | elapsed | |
| M3D_Wrapper | 0.622 | 0.018 | 0.650 | |
| M3D_Wrapper_lite | 0.724 | 0.012 | 0.756 | |
| determineGroupComps | 0.347 | 0.012 | 0.364 | |
| findComps | 0.352 | 0.017 | 0.372 | |
| median_freq | 0.001 | 0.000 | 0.001 | |
| plotCoverageSampleProfiles | 0.237 | 0.009 | 0.255 | |
| plotMethProfile | 0.336 | 0.014 | 0.356 | |
| plotMethSampleProfiles | 0.593 | 0.015 | 0.617 | |
| pvals | 0.499 | 0.039 | 0.541 | |
| pvals_lite | 0.559 | 0.023 | 0.596 | |
| readBedFiles | 0 | 0 | 0 | |
| readBedRaw | 0.000 | 0.001 | 0.000 | |