Rdisop 1.35.0
Steffen Neumann
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rdisop | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rdisop_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rdisop.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rdisop/DESCRIPTION’ ... OK
* this is package ‘Rdisop’ version ‘1.35.0’
* 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 ‘Rdisop’ 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 ... NOTE
Package in Depends field not imported from: ‘RcppClassic’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘Rdisop/libs/Rdisop.so’:
Found ‘_rand’, possibly from ‘rand’ (C)
Object: ‘imslib/src/ims/utils/distribution.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.R’
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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/Rdisop.Rcheck/00check.log’
for details.
* installing *source* package ‘Rdisop’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c disop.cpp -o disop.o
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
bool parityeven = !parityodd;
^
disop.cpp:181:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
int number_molecules_shown = 100;
^
disop.cpp:825:59: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
const char *symbol = CHAR(Rf_asChar(getListElement(l, "name")));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:463:25: note: expanded from macro 'CHAR'
#define CHAR(x) R_CHAR(x)
^
disop.cpp:827:80: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
nominal_mass_type nominalmass = (nominal_mass_type) REAL(getListElement(l, "mass"))[0];
^
disop.cpp:829:38: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
SEXP isotope = getListElement(l, "isotope");
^
disop.cpp:831:57: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
int numisotopes = Rf_length(getListElement(isotope, "mass"));
^
disop.cpp:832:49: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
double *mass = REAL(getListElement(isotope, "mass"));
^
disop.cpp:833:54: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
double *abundance = REAL(getListElement(isotope, "abundance"));
^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
for (; letter_pos < last_pos &&
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: note: place parentheses around the '&&' expression to silence this warning
for (; letter_pos < last_pos &&
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I./imslib/src/ -fPIC -Wall -mtune=core2 -g -O2 -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.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 Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppClassic/lib/libRcppClassic.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/Rdisop.Rcheck/Rdisop/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 (Rdisop)