Tom Mayo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/M3D |
| Branch: RELEASE_3_9 |
| Last Commit: 7a450e3 |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:53:41 -0400 (Wed, 16 Oct 2019).
| Package 897/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| M3D 1.18.0 Tom Mayo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: M3D |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3D_1.18.0.tar.gz |
| StartedAt: 2019-10-16 04:10:22 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:16:29 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 367.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: M3D.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3D.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3D_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3D.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/M3D.Rcheck/00check.log’
for details.
M3D.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL M3D ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘M3D’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c cpp_fns.cpp -o cpp_fns.o clang++ -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 M3D.so RcppExports.o cpp_fns.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-M3D/00new/M3D/libs ** R ** data ** 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 (M3D)
M3D.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
17.384 1.625 18.958
M3D.Rcheck/M3D-Ex.timings
| name | user | system | elapsed | |
| M3D_Wrapper | 1.364 | 0.032 | 1.397 | |
| M3D_Wrapper_lite | 0.251 | 0.021 | 0.272 | |
| determineGroupComps | 0.595 | 0.033 | 0.628 | |
| findComps | 0.496 | 0.038 | 0.535 | |
| median_freq | 0.000 | 0.000 | 0.001 | |
| plotCoverageSampleProfiles | 0.328 | 0.029 | 0.358 | |
| plotMethProfile | 0.249 | 0.014 | 0.263 | |
| plotMethSampleProfiles | 0.256 | 0.015 | 0.272 | |
| pvals | 0.741 | 0.080 | 0.822 | |
| pvals_lite | 0.655 | 0.053 | 0.707 | |
| readBedFiles | 0 | 0 | 0 | |
| readBedRaw | 0 | 0 | 0 | |