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CHECK report for IPPD on celaya2

This page was generated on 2020-01-16 13:33:00 -0500 (Thu, 16 Jan 2020).

Package 859/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IPPD 1.35.0
Martin Slawski
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/IPPD
Branch: master
Last Commit: f00e532
Last Changed Date: 2019-10-29 13:35:21 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: IPPD
Version: 1.35.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IPPD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IPPD_1.35.0.tar.gz
StartedAt: 2020-01-16 05:41:15 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 05:43:24 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 128.1 seconds
RetCode: 0
Status:  OK 
CheckDir: IPPD.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IPPD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IPPD_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/IPPD.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IPPD/DESCRIPTION’ ... OK
* this is package ‘IPPD’ 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 ‘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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getPeaklist 28.434  2.203  30.639
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/IPPD.Rcheck/00check.log’
for details.



Installation output

IPPD.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IPPD
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘IPPD’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_IPPD.c -o R_init_IPPD.o
R_init_IPPD.c:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  NULL
  ^~~~
  {   }
/usr/local/clang8/lib/clang/8.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^~~~~~~~~~
1 warning generated.
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 IPPD.so R_init_IPPD.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-IPPD/00new/IPPD/libs
** R
** data
** 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 (IPPD)

Tests output


Example timings

IPPD.Rcheck/IPPD-Ex.timings

nameusersystemelapsed
fitModelParameters2.0730.2342.310
getPeaklist28.434 2.20330.639
myo5000.0840.0140.099
toyspectrum0.2100.0410.251