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CHECK report for SIM on tokay1

This page was generated on 2019-04-13 11:20:44 -0400 (Sat, 13 Apr 2019).

Package 1448/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIM 1.52.0
Renee X. de Menezes
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/SIM
Branch: RELEASE_3_8
Last Commit: 0d16b7e
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SIM
Version: 1.52.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SIM_1.52.0.tar.gz
StartedAt: 2019-04-13 05:33:05 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:36:46 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 220.4 seconds
RetCode: 0
Status:  OK  
CheckDir: SIM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SIM.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SIM_1.52.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SIM.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 'SIM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIM' version '1.52.0'
* 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 'SIM' 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
* 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' call to 'biomaRt' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'quantreg'
  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
File 'SIM/R/zzz.R':
  .onAttach calls:
    library.dynam("SIM", pkg, lib)

See section 'Good practice' in '?.onAttach'.

dependent.heatmap: warning in get(as.character(adjust[[2]]), env =
  attr(adjust, ".Environment")): partial argument match of 'env' to
  'envir'
sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")):
  partial argument match of 'env' to 'envir'
sim.update.chrom.table: warning in factor(table$name, level = c(1:22,
  "X", "Y")): partial argument match of 'level' to 'levels'
assemble.data: no visible global function definition for 'data'
assemble.data: no visible binding for global variable 'chrom.table'
convertGenomicRegion: no visible global function definition for 'data'
convertGenomicRegion: no visible binding for global variable
  'chrom.table'
dependent.heatmap: no visible global function definition for 'strwidth'
getoverlappingregions: no visible global function definition for
  'useMart'
getoverlappingregions: no visible global function definition for
  'getBM'
impute.nas.by.surrounding: no visible binding for global variable
  'median'
impute.nas.by.surrounding: no visible global function definition for
  'na.omit'
independent.heatmap: no visible global function definition for
  'strwidth'
link.metadata: no visible binding for global variable 'expr.data'
link.metadata: no visible binding for global variable 'hgu133plus2CHR'
link.metadata: no visible binding for global variable
  'hgu133plus2CHRLOC'
link.metadata: no visible binding for global variable
  'hgu133plus2SYMBOL'
link.metadata: no visible global function definition for 'aggregate'
plotCytobands: no visible global function definition for 'data'
plotCytobands: no visible binding for global variable 'chrom.table'
quantsmooth.plot: no visible global function definition for 'rainbow'
showProgress: no visible global function definition for 'flush.console'
sim.plot.overlapping.indep.dep.features: no visible global function
  definition for 'box'
sim.plot.pvals.on.genome: no visible global function definition for
  'data'
sim.plot.pvals.on.genome: no visible binding for global variable
  'chrom.table'
sim.plot.zoom.in: no visible global function definition for
  'flush.console'
sim.plot.zoom.in: no visible global function definition for 'dev.new'
sim.plot.zscore.heatmap: no visible global function definition for
  'colorRampPalette'
sim.update.chrom.table: no visible global function definition for
  'dbConnect'
sim.update.chrom.table: no visible global function definition for
  'MySQL'
sim.update.chrom.table: no visible global function definition for
  'dbGetQuery'
tabulate.top.dep.features: no visible global function definition for
  'na.omit'
tabulate.top.dep.features: no visible global function definition for
  'write.table'
tabulate.top.indep.features: no visible global function definition for
  'na.omit'
tabulate.top.indep.features: no visible global function definition for
  'write.table'
validColumn: no visible global function definition for 'type.convert'
Undefined global functions or variables:
  MySQL aggregate box chrom.table colorRampPalette data dbConnect
  dbGetQuery dev.new expr.data flush.console getBM hgu133plus2CHR
  hgu133plus2CHRLOC hgu133plus2SYMBOL median na.omit rainbow strwidth
  type.convert useMart write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "rainbow")
  importFrom("graphics", "box", "strwidth")
  importFrom("stats", "aggregate", "median", "na.omit")
  importFrom("utils", "data", "flush.console", "type.convert",
             "write.table")
to your NAMESPACE file.
* 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-3.8-bioc/R/library/SIM/libs/i386/SIM.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
SIM-package         6.91   0.07    6.97
integrated.analysis 5.78   0.00    5.78
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
SIM-package         7.18   0.12    7.32
integrated.analysis 5.88   0.00    5.88
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/SIM.Rcheck/00check.log'
for details.



Installation output

SIM.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/SIM_1.52.0.tar.gz && rm -rf SIM.buildbin-libdir && mkdir SIM.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SIM.buildbin-libdir SIM_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SIM_1.52.0.zip && rm SIM_1.52.0.tar.gz SIM_1.52.0.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
100  269k  100  269k    0     0  7234k      0 --:--:-- --:--:-- --:--:-- 7918k

install for i386

* installing *source* package 'SIM' ...
** 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 withinWindow.c -o withinWindow.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.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/SIM.buildbin-libdir/SIM/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SIM'
    finding HTML links ... done
    RESOURCERER.annotation.to.ID            html  
    SIM-package                             html  
    acgh.data                               html  
    assemble.data                           html  
    chrom.table                             html  
    expr.data                               html  
    getoverlappingregions                   html  
    impute.nas.by.surrounding               html  
    integrated.analysis                     html  
    link.metadata                           html  
    samples                                 html  
    sim.plot.overlapping.indep.dep.features
                                            html  
    sim.plot.pvals.on.genome                html  
    sim.plot.pvals.on.region                html  
    sim.plot.zoom.in                        html  
    sim.plot.zscore.heatmap                 html  
    sim.update.chrom.table                  html  
    tabulate.pvals                          html  
    tabulate.top.dep.features               html  
    tabulate.top.indep.features             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SIM' ...
** 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 withinWindow.c -o withinWindow.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.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/SIM.buildbin-libdir/SIM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SIM' as SIM_1.52.0.zip
* DONE (SIM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SIM' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

SIM.Rcheck/examples_i386/SIM-Ex.timings

nameusersystemelapsed
RESOURCERER.annotation.to.ID000
SIM-package6.910.076.97
acgh.data0.020.000.01
assemble.data0.040.000.05
chrom.table0.020.000.02
expr.data000
getoverlappingregions000
impute.nas.by.surrounding000
integrated.analysis5.780.005.78
link.metadata000
samples000
sim.plot.overlapping.indep.dep.features0.050.000.05
sim.plot.pvals.on.genome0.110.030.14
sim.plot.pvals.on.region000
sim.plot.zoom.in0.230.000.24
sim.plot.zscore.heatmap0.500.020.51
sim.update.chrom.table000
tabulate.pvals0.020.000.02
tabulate.top.dep.features0.010.000.01
tabulate.top.indep.features0.020.020.03

SIM.Rcheck/examples_x64/SIM-Ex.timings

nameusersystemelapsed
RESOURCERER.annotation.to.ID000
SIM-package7.180.127.32
acgh.data0.000.020.01
assemble.data0.020.010.03
chrom.table000
expr.data000
getoverlappingregions000
impute.nas.by.surrounding000
integrated.analysis5.880.005.88
link.metadata000
samples0.000.020.01
sim.plot.overlapping.indep.dep.features0.060.000.07
sim.plot.pvals.on.genome0.140.020.15
sim.plot.pvals.on.region000
sim.plot.zoom.in0.200.030.24
sim.plot.zscore.heatmap0.380.000.37
sim.update.chrom.table000
tabulate.pvals000
tabulate.top.dep.features0.010.000.02
tabulate.top.indep.features0.020.000.01