Charles Warden
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/COHCAP |
| Branch: RELEASE_3_8 |
| Last Commit: 5bd856f |
| Last Changed Date: 2018-11-09 12:36:45 -0400 (Fri, 09 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:57:18 -0400 (Tue, 16 Apr 2019).
| Package 307/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| COHCAP 1.28.1 Charles Warden
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: COHCAP |
| Version: 1.28.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:COHCAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings COHCAP_1.28.1.tar.gz |
| StartedAt: 2019-04-15 23:09:19 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:10:22 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 63.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COHCAP.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:COHCAP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings COHCAP_1.28.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/COHCAP.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COHCAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COHCAP’ version ‘1.28.1’
* 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 ‘COHCAP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
COHCAP.annotate: no visible binding for global variable
‘COHCAP.450k.UCSC’
COHCAP.annotate: no visible binding for global variable
‘COHCAP.450k.HMM’
COHCAP.annotate: no visible binding for global variable ‘COHCAP.27k’
COHCAP.integrate.avg.by.island: no visible binding for global variable
‘na.rm’
cor.test.est: no visible binding for global variable ‘na.rm’
cor.test.pvalue: no visible binding for global variable ‘na.rm’
Undefined global functions or variables:
COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC na.rm
* 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 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
Examples with CPU or elapsed time > 5s
user system elapsed
COHCAP.integrate.avg.by.island 5.377 0.532 6.033
COHCAP.integrate.avg.by.site 4.544 0.399 5.048
* 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-3.8-bioc/meat/COHCAP.Rcheck/00check.log’
for details.
COHCAP.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL COHCAP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘COHCAP’ ...
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/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/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Rcpp_BH_ANOVA.cpp -o Rcpp_BH_ANOVA.o
In file included from Rcpp_BH_ANOVA.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/distributions/fisher_f.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/beta.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Rcpp_BH_ttest.cpp -o Rcpp_BH_ttest.o
In file included from Rcpp_BH_ttest.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/distributions/students_t.hpp:16:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/beta.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/special_functions/gamma.hpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/constants/constants.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:44:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
#define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
1 warning generated.
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 COHCAP.so RcppExports.o Rcpp_BH_ANOVA.o Rcpp_BH_ttest.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/COHCAP/libs
** R
** 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
* DONE (COHCAP)
COHCAP.Rcheck/COHCAP-Ex.timings
| name | user | system | elapsed | |
| COHCAP.BSSeq.preprocess | 0.030 | 0.011 | 0.047 | |
| COHCAP.BSSeq_V2.methyl.table | 0.022 | 0.002 | 0.025 | |
| COHCAP.annotate | 2.040 | 0.118 | 2.189 | |
| COHCAP.avg.by.island | 4.382 | 0.392 | 4.852 | |
| COHCAP.avg.by.site | 4.050 | 0.328 | 4.460 | |
| COHCAP.denovo | 3.500 | 0.251 | 3.805 | |
| COHCAP.integrate.avg.by.island | 5.377 | 0.532 | 6.033 | |
| COHCAP.integrate.avg.by.site | 4.544 | 0.399 | 5.048 | |
| COHCAP.qc | 1.748 | 0.091 | 1.872 | |
| COHCAP.reformatFinalReport | 0.010 | 0.001 | 0.015 | |
| COHCAP.site | 3.281 | 0.222 | 3.551 | |