Ioannis Vardaxis
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MACPET |
| Branch: master |
| Last Commit: 8bdde99 |
| Last Changed Date: 2019-03-31 05:30:40 -0400 (Sun, 31 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:19:52 -0400 (Tue, 09 Apr 2019).
| Package 887/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MACPET 1.3.3 Ioannis Vardaxis
| 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: MACPET |
| Version: 1.3.3 |
| 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_1.3.3.tar.gz |
| StartedAt: 2019-04-09 03:10:30 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:17:00 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 389.7 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_1.3.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MACPET.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.3’
* 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 8.692 3.033 14.095
PeaksToGRanges 5.291 2.921 0.135
plot 6.777 0.130 6.909
* 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-3.9-bioc/meat/MACPET.Rcheck/00check.log’
for details.
MACPET.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MACPET
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MACPET’ ...
** 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" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/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/3.6/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:85:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:85:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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:125:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:125:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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:162:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:162:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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:201:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:201:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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:238:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/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:238:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:275:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:275:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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:311:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/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:311:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:351:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:351:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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:389:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/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:389:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:428:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/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:428:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:465:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:465:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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:504:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/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:504:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:544:1: warning: unused variable 'stop_sym' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/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:544:1: warning: unused variable 'nprot' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:579:1: warning: unused variable 'nprot' [-Wunused-variable]
BEGIN_RCPP
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/macros/macros.h:32:9: note: expanded from macro 'BEGIN_RCPP'
int nprot = 0; \
^
RcppExports.cpp:579:1: warning: unused variable 'stop_sym' [-Wunused-variable]
/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.6/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/3.6/Resources/library/00LOCK-MACPET/00new/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 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 (MACPET)
MACPET.Rcheck/MACPET-Ex.timings
| name | user | system | elapsed | |
| AnalysisStatistics | 0.112 | 0.010 | 0.125 | |
| ConvertToPE_BAM | 4.325 | 0.413 | 4.773 | |
| ConvertToPSelf | 0.380 | 0.017 | 0.397 | |
| GetShortestPath | 0.136 | 0.025 | 0.165 | |
| GetSignInteractions | 0.099 | 0.018 | 0.119 | |
| MACPETUlt | 8.692 | 3.033 | 14.095 | |
| PeaksToGRanges | 5.291 | 2.921 | 0.135 | |
| PeaksToNarrowPeak | 0.120 | 0.057 | 0.177 | |
| TagsToGInteractions | 0.111 | 0.020 | 0.130 | |
| exportPeaks | 0.012 | 0.004 | 0.016 | |
| plot | 6.777 | 0.130 | 6.909 | |
| summary | 0.885 | 0.018 | 0.905 | |