Pierre Neuvial
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MANOR |
| Branch: RELEASE_3_9 |
| Last Commit: 8eeb0c3 |
| Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:45:41 -0400 (Wed, 16 Oct 2019).
| Package 910/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MANOR 1.56.0 Pierre Neuvial
| 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: MANOR |
| Version: 1.56.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MANOR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MANOR_1.56.0.tar.gz |
| StartedAt: 2019-10-16 04:14:09 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:14:57 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 48.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MANOR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MANOR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MANOR_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MANOR.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 ‘MANOR/DESCRIPTION’ ... OK * this is package ‘MANOR’ version ‘1.56.0’ * 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 ‘MANOR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘GLAD’ A package should be listed in only one of these fields. * 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 ... NOTE Found the following apparent S3 methods exported but not registered: arrayTrend.arrayCGH arrayTrend.default detectSB.arrayCGH flag.summary.arrayCGH flag.summary.default genome.plot.arrayCGH genome.plot.default html.report.arrayCGH html.report.default nem.arrayCGH nem.default norm.arrayCGH print.flag report.plot.arrayCGH report.plot.default sort.arrayCGH See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * 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 compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/MANOR/libs/MANOR.so’: Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_srand’, possibly from ‘srand’ (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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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/MANOR.Rcheck/00check.log’ for details.
MANOR.Rcheck/00install.out
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MANOR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MANOR’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Rnem_arg.c -o Rnem_arg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Rnem_exe.c -o Rnem_exe.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c exememo.c -o exememo.o
exememo.c:40:13: warning: variable 'msg' is uninitialized when used here [-Wuninitialized]
sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
^~~
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/secure/_stdio.h:47:28: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^~~
exememo.c:39:14: note: initialize the variable 'msg' to silence this warning
char* msg;
^
= NULL
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nem_alg.c -o nem_alg.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nem_hlp.c -o nem_hlp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nem_mod.c -o nem_mod.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nem_nei.c -o nem_nei.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nem_rnd.c -o nem_rnd.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c nem_ver.c -o nem_ver.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 MANOR.so Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-MANOR/00new/MANOR/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 (MANOR)
MANOR.Rcheck/MANOR-Ex.timings
| name | user | system | elapsed | |
| arrayTrend | 0.448 | 0.038 | 0.487 | |
| detectSB | 0.383 | 0.033 | 0.417 | |
| flag.arrayCGH | 1.662 | 0.060 | 1.722 | |
| flag.summary | 0.149 | 0.015 | 0.165 | |
| flags | 0.148 | 0.018 | 0.167 | |
| genome.plot | 0.454 | 0.019 | 0.474 | |
| import | 0.218 | 0.009 | 0.230 | |
| nem | 1.308 | 0.015 | 1.325 | |
| norm | 1.052 | 0.061 | 1.114 | |
| qscore.arrayCGH | 0.139 | 0.015 | 0.155 | |
| qscore.summary | 0.812 | 0.024 | 0.836 | |
| qscores | 0.794 | 0.025 | 0.821 | |
| report.plot | 0.930 | 0.070 | 1.003 | |
| sort | 0.197 | 0.023 | 0.227 | |
| spatial | 0.289 | 0.025 | 0.319 | |
| to.flag | 0.451 | 0.037 | 0.488 | |