Martin Slawski
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/IPPD |
| Branch: RELEASE_3_8 |
| Last Commit: 6aea9f2 |
| Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:26 -0400 (Sat, 13 Apr 2019).
| Package 792/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IPPD 1.30.0 Martin Slawski
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: IPPD |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IPPD.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings IPPD_1.30.0.tar.gz |
| StartedAt: 2019-04-13 03:14:10 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:17:26 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 195.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IPPD.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IPPD.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings IPPD_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/IPPD.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
* 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 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-3.8-bioc/R/library/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getPeaklist 26.63 1.43 28.06
fitModelParameters 8.92 0.07 8.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getPeaklist 22.69 1.83 24.52
* 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-3.8-bioc/meat/IPPD.Rcheck/00check.log'
for details.
IPPD.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/IPPD_1.30.0.tar.gz && rm -rf IPPD.buildbin-libdir && mkdir IPPD.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IPPD.buildbin-libdir IPPD_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL IPPD_1.30.0.zip && rm IPPD_1.30.0.tar.gz IPPD_1.30.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 1050k 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
100 1050k 100 1050k 0 0 926k 0 0:00:01 0:00:01 --:--:-- 929k
install for i386
* installing *source* package 'IPPD' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'IPPD'
finding HTML links ... done
IPPD-package html
analyzeLCMS html
fitModelParameters html
getPeaklist html
internals html
modelfit-class html
myo500 html
peaklist-class html
read.mzXML html
sweepline html
toyspectrum html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'IPPD' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/IPPD.buildbin-libdir/IPPD/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IPPD' as IPPD_1.30.0.zip
* DONE (IPPD)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'IPPD' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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IPPD.Rcheck/examples_i386/IPPD-Ex.timings
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IPPD.Rcheck/examples_x64/IPPD-Ex.timings
|