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BioC 3.5: CHECK report for pqsfinder on toluca2

This page was generated on 2017-04-23 14:41:35 -0400 (Sun, 23 Apr 2017).

Package 998/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 1.3.21
Jiri Hon
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pqsfinder
Last Changed Rev: 128591 / Revision: 129046
Last Changed Date: 2017-04-12 10:09:23 -0400 (Wed, 12 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pqsfinder
Version: 1.3.21
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pqsfinder_1.3.21.tar.gz
StartedAt: 2017-04-23 08:08:14 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 08:10:38 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 143.9 seconds
RetCode: 0
Status:  OK 
CheckDir: pqsfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pqsfinder_1.3.21.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘1.3.21’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/boost_regex/c_regex_traits.o src/boost_regex/cpp_regex_traits.o
  src/boost_regex/cregex.o src/boost_regex/fileiter.o
  src/boost_regex/icu.o src/boost_regex/instances.o
  src/boost_regex/posix_api.o src/boost_regex/regex.o
  src/boost_regex/regex_debug.o src/boost_regex/regex_raw_buffer.o
  src/boost_regex/regex_traits_defaults.o
  src/boost_regex/static_mutex.o src/boost_regex/usinstances.o
  src/boost_regex/w32_regex_traits.o src/boost_regex/wc_regex_traits.o
  src/boost_regex/wide_posix_api.o src/boost_regex/winstances.o
Object files/libraries should not be included in a source package.
* 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 ‘pqsfinder’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    lib  10.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
* 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 loading without being on the library search path ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.

pqsfinder.Rcheck/00install.out:

* installing *source* package ‘pqsfinder’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c pqsfinder.cpp -o pqsfinder.o
In file included from pqsfinder.cpp:16:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from pqsfinder.cpp:16:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from pqsfinder.cpp:22:
./pqs_cache.h:43:63: warning: field 'max_len' will be initialized after field 'f' [-Wreorder]
    entry(const entry &obj) : score(obj.score), len(obj.len), max_len(obj.max_len), f(obj.f) {
                                                              ^
pqsfinder.cpp:244:32: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  bool pqs_ends[RUN_CNT][2] = {0};
                               ^
                               {}
pqsfinder.cpp:336:7: warning: unused variable 'd1' [-Wunused-variable]
  int d1 = (l[0] - mean)*(l[0] - mean);
      ^
pqsfinder.cpp:337:7: warning: unused variable 'd2' [-Wunused-variable]
  int d2 = (l[1] - mean)*(l[1] - mean);
      ^
pqsfinder.cpp:338:7: warning: unused variable 'd3' [-Wunused-variable]
  int d3 = (l[2] - mean)*(l[2] - mean);
      ^
7 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
In file included from boost_regex/cregex.cpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/cregex.cpp:22:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/icu.cpp -o boost_regex/icu.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/instances.cpp -o boost_regex/instances.o
In file included from boost_regex/instances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/instances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
In file included from boost_regex/posix_api.cpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/posix_api.cpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o
In file included from boost_regex/regex.cpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/regex.cpp:24:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
In file included from boost_regex/wide_posix_api.cpp:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/wide_posix_api.cpp:25:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
In file included from boost_regex/winstances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from boost_regex/winstances.cpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
mkdir -p "/Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib"
ar rs "/Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating archive /Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib/libboost_regex.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib/libboost_regex.a(icu.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib/libboost_regex.a(regex_debug.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib/libboost_regex.a(usinstances.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib/libboost_regex.a(w32_regex_traits.o) has no symbols
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 pqsfinder.so RcppExports.o pqsfinder.o /Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/pqsfinder.Rcheck/pqsfinder/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pqsfinder)

pqsfinder.Rcheck/pqsfinder-Ex.timings:

nameusersystemelapsed
PQSViews0.2140.0170.232
density-PQSViews-method0.1720.0000.183
maxScores-PQSViews-method0.040.000.04
maxScores0.0030.0000.003
pqsfinder0.0880.0000.105
score-PQSViews-method0.0220.0010.022
strand-PQSViews-method0.0220.0000.023