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BioC 3.5: CHECK report for reb on tokay2

This page was generated on 2017-08-16 13:19:02 -0400 (Wed, 16 Aug 2017).

Package 1089/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
reb 1.54.0
Karl J. Dykema
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/reb
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: reb
Version: 1.54.0
Command: rm -rf reb.buildbin-libdir reb.Rcheck && mkdir reb.buildbin-libdir reb.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=reb.buildbin-libdir reb_1.54.0.tar.gz >reb.Rcheck\00install.out 2>&1 && cp reb.Rcheck\00install.out reb-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=reb.buildbin-libdir --install="check:reb-install.out" --force-multiarch --no-vignettes --timings reb_1.54.0.tar.gz
StartedAt: 2017-08-16 02:20:32 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:23:11 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 159.3 seconds
RetCode: 0
Status:  OK  
CheckDir: reb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf reb.buildbin-libdir reb.Rcheck && mkdir reb.buildbin-libdir reb.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=reb.buildbin-libdir reb_1.54.0.tar.gz >reb.Rcheck\00install.out 2>&1 && cp reb.Rcheck\00install.out reb-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=reb.buildbin-libdir --install="check:reb-install.out" --force-multiarch --no-vignettes --timings reb_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/reb.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 'reb/DESCRIPTION' ... OK
* this is package 'reb' version '1.54.0'
* 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 'reb' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Missing object imported by a ':::' call: 'Biobase:::EXPRSET_DEPR_MSG'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.MAP2chromLoc: warning in mget(subnames, env = chrEnv, ifnotfound =
  NA): partial argument match of 'env' to 'envir'
rmAmbigMappings: warning in ls(env = get(package)): partial argument
  match of 'env' to 'envir'
.genMeanMatrix: no visible global function definition for 't.test'
buildChromCytoband: no visible global function definition for 'new'
buildChromCytoband: no visible binding for global variable
  'Hs.cytoband'
buildChromCytoband: no visible binding for global variable
  'Rn.cytoband'
buildChromCytoband: no visible binding for global variable
  'Mm.cytoband'
buildChromMap: no visible global function definition for 'new'
cgma: no visible binding for global variable 't.test'
cset2band: no visible global function definition for 'aggregate'
fromRevIsh: no visible binding for global variable 'vai.chr'
reb: no visible global function definition for 'supsmu'
reb: no visible global function definition for 'lowess'
reb: no visible global function definition for 'approx'
regmap: no visible global function definition for 'par'
regmap: no visible global function definition for 'layout'
regmap: no visible global function definition for 'image'
regmap: no visible global function definition for 'axis'
smoothByRegion: no visible global function definition for 'supsmu'
smoothByRegion: no visible global function definition for 'lowess'
smoothByRegion: no visible global function definition for 'approx'
summarizeByRegion: no visible binding for global variable 't.test'
tBinomTest: no visible global function definition for 'binom.test'
writeGFF3: no visible global function definition for 'write.table'
Undefined global functions or variables:
  Hs.cytoband Mm.cytoband Rn.cytoband aggregate approx axis binom.test
  image layout lowess new par supsmu t.test vai.chr write.table
Consider adding
  importFrom("graphics", "axis", "image", "layout", "par")
  importFrom("methods", "new")
  importFrom("stats", "aggregate", "approx", "binom.test", "lowess",
             "supsmu", "t.test")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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-3.5-bioc/meat/reb.buildbin-libdir/reb/libs/i386/reb.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

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
cset2band 5.21    0.3     5.5
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/reb.Rcheck/00check.log'
for details.


reb.Rcheck/00install.out:


install for i386

* installing *source* package 'reb' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c movbin.c -o movbin.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o reb.dll tmp.def movbin.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/reb.buildbin-libdir/reb/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 'reb' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c movbin.c -o movbin.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o reb.dll tmp.def movbin.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/reb.buildbin-libdir/reb/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'reb' as reb_1.54.0.zip
* DONE (reb)

reb.Rcheck/examples_i386/reb-Ex.timings:

nameusersystemelapsed
absMax000
buildChromCytoband0.000.010.68
buildChromMap000
cset2band5.210.305.50
fromRevIsh2.780.062.85
isAbnormal000
mcr.eset0.060.020.07
movbin0.050.000.05
movt0.400.000.41
naMean000
regmap0.020.000.01
revish0.120.000.13
rmAmbigMappings000
smoothByRegion2.740.092.83
summarizeByRegion000
tBinomTest0.000.000.01
writeGFF30.080.020.10

reb.Rcheck/examples_x64/reb-Ex.timings:

nameusersystemelapsed
absMax000
buildChromCytoband000
buildChromMap000
cset2band4.640.194.82
fromRevIsh3.080.043.13
isAbnormal000
mcr.eset0.070.020.09
movbin0.050.000.05
movt0.750.000.75
naMean000
regmap0.020.000.02
revish0.180.020.20
rmAmbigMappings000
smoothByRegion4.080.094.18
summarizeByRegion000
tBinomTest000
writeGFF30.110.000.11