IPPD 1.25.0
Martin Slawski
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IPPD | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf IPPD.buildbin-libdir IPPD.Rcheck && mkdir IPPD.buildbin-libdir IPPD.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IPPD.buildbin-libdir IPPD_1.25.0.tar.gz >IPPD.Rcheck\00install.out 2>&1 && cp IPPD.Rcheck\00install.out IPPD-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IPPD.buildbin-libdir --install="check:IPPD-install.out" --force-multiarch --no-vignettes --timings IPPD_1.25.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IPPD/DESCRIPTION' ... OK
* this is package 'IPPD' version '1.25.0'
* 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 whether package 'IPPD' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL (version 2 or later)
Standardizable: TRUE
Standardized license specification:
GPL (>= 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'MASS' 'Matrix' 'bitops'
Please remove these calls from your code.
Package in Depends field not imported from: 'bitops'
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 ... NOTE
analyzeLCMS: no visible global function definition for 'read.table'
base64decode: no visible global function definition for 'bitOr'
base64decode: no visible global function definition for 'bitShiftL'
base64decode: no visible global function definition for 'bitShiftR'
base64decode: no visible global function definition for 'bitAnd'
getPeaklist,numeric-numeric: no visible global function definition for
'data'
getPeaklist,numeric-numeric: no visible binding for global variable
'tableaveragine'
threshold,peaklist: no visible binding for global variable 'peaklist'
visualize,modelfit-missing-missing: no visible global function
definition for 'lines'
visualize,modelfit-missing-missing: no visible global function
definition for 'par'
visualize,peaklist-numeric-numeric: no visible global function
definition for 'layout'
visualize,peaklist-numeric-numeric: no visible global function
definition for 'lines'
visualize,peaklist-numeric-numeric: no visible global function
definition for 'matlines'
Undefined global functions or variables:
bitAnd bitOr bitShiftL bitShiftR data layout lines matlines par
peaklist read.table tableaveragine
Consider adding
importFrom("graphics", "layout", "lines", "matlines", "par")
importFrom("utils", "data", "read.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: analyzeLCMS.Rd:50: Dropping empty section \examples
prepare_Rd: read.mzXML.Rd:21: Dropping empty section \examples
prepare_Rd: sweepline.Rd:40: Dropping empty section \examples
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/i386/IPPD.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getPeaklist 27.88 1.57 29.45
fitModelParameters 7.87 0.05 7.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getPeaklist 26.92 1.61 28.57
* 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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'IPPD' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_IPPD.c -o R_init_IPPD.o
R_init_IPPD.c:29:1: warning: missing braces around initializer [-Wmissing-braces]
};
^
R_init_IPPD.c:29:1: warning: (near initialization for 'cmethods[10]') [-Wmissing-braces]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o IPPD.dll tmp.def R_init_IPPD.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'IPPD' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_IPPD.c -o R_init_IPPD.o
R_init_IPPD.c:29:1: warning: missing braces around initializer [-Wmissing-braces]
};
^
R_init_IPPD.c:29:1: warning: (near initialization for 'cmethods[10]') [-Wmissing-braces]
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o IPPD.dll tmp.def R_init_IPPD.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IPPD' as IPPD_1.25.0.zip
* DONE (IPPD)