Ioannis Vardaxis
| Snapshot Date: 2019-03-17 17:02:07 -0400 (Sun, 17 Mar 2019) |
| URL: https://git.bioconductor.org/packages/MACPET |
| Branch: RELEASE_3_8 |
| Last Commit: 7c55f69 |
| Last Changed Date: 2018-10-30 11:42:08 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-03-18 11:34:15 -0400 (Mon, 18 Mar 2019).
| Package 863/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| MACPET 1.2.0 Ioannis Vardaxis
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | ERROR | ERROR | skipped | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | |
| Package: MACPET |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MACPET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MACPET_1.2.0.tar.gz |
| StartedAt: 2019-03-18 01:02:07 -0400 (Mon, 18 Mar 2019) |
| EndedAt: 2019-03-18 01:07:08 -0400 (Mon, 18 Mar 2019) |
| EllapsedTime: 300.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MACPET.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MACPET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MACPET_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MACPET.Rcheck’
* using R version 3.5.2 Patched (2018-12-20 r75875)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MACPET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MACPET’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘MACPET’ 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 ... 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 R/sysdata.rda ... 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
MACPETUlt 6.938 1.554 10.422
plot 6.442 0.084 6.833
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/MACPET.Rcheck/00check.log’
for details.
MACPET.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MACPET
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MACPET’ ...
** libs
clang++ -std=gnu++11 -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/bigmemory/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
RcppExports.cpp:46:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:46:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:81:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:81:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:117:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:117:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:150:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:150:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:185:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:185:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:218:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:218:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:251:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:251:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:283:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:283:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:319:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:319:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:353:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:353:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:388:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:388:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:421:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:421:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:456:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:456:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:492:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:492:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
RcppExports.cpp:523:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:523:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/macros/macros.h:36:17: note: expanded from macro 'BEGIN_RCPP'
static SEXP stop_sym = Rf_install("stop"); \
^
30 warnings generated.
clang++ -std=gnu++11 -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/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Stage_0_FastqFilteringSubFunctions.cpp -o Stage_0_FastqFilteringSubFunctions.o
clang++ -std=gnu++11 -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/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Stage_3_PeakFinderSubFunctions.cpp -o Stage_3_PeakFinderSubFunctions.o
clang++ -std=gnu++11 -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/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Stage_4_InteractionsSubFunctions.cpp -o Stage_4_InteractionsSubFunctions.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 MACPET.so RcppExports.o Stage_0_FastqFilteringSubFunctions.o Stage_3_PeakFinderSubFunctions.o Stage_4_InteractionsSubFunctions.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/MACPET/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 (MACPET)
MACPET.Rcheck/MACPET-Ex.timings
| name | user | system | elapsed | |
| AnalysisStatistics | 0.227 | 0.008 | 0.239 | |
| ConvertToPE_BAM | 3.778 | 0.244 | 4.431 | |
| ConvertToPSelf | 0.295 | 0.032 | 0.413 | |
| GetShortestPath | 0.125 | 0.016 | 0.143 | |
| GetSignInteractions | 0.088 | 0.013 | 0.101 | |
| MACPETUlt | 6.938 | 1.554 | 10.422 | |
| PeaksToGRanges | 2.018 | 1.016 | 0.097 | |
| PeaksToNarrowPeak | 0.144 | 0.033 | 0.177 | |
| TagsToGInteractions | 0.095 | 0.015 | 0.110 | |
| exportPeaks | 0.011 | 0.004 | 0.015 | |
| plot | 6.442 | 0.084 | 6.833 | |
| summary | 0.913 | 0.011 | 0.959 | |