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CHECK report for SIM on machv2

This page was generated on 2020-10-17 11:59:38 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SIM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1661/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIM 1.58.0
Renee X. de Menezes
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SIM
Branch: RELEASE_3_11
Last Commit: d1b1301
Last Changed Date: 2020-04-27 14:17:28 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SIM
Version: 1.58.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIM_1.58.0.tar.gz
StartedAt: 2020-10-17 05:22:24 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:25:32 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 187.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SIM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SIM_1.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SIM.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIM’ version ‘1.58.0’
* 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 ‘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
* 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 binding for global variable ‘chrom.table’
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’
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’
plotCytobands: no visible binding for global variable ‘chrom.table’
sim.plot.overlapping.indep.dep.features: no visible global function
  definition for ‘box’
sim.plot.pvals.on.genome: no visible binding for global variable
  ‘chrom.table’
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’
Undefined global functions or variables:
  MySQL box chrom.table dbConnect dbGetQuery expr.data getBM
  hgu133plus2CHR hgu133plus2CHRLOC hgu133plus2SYMBOL strwidth useMart
Consider adding
  importFrom("graphics", "box", "strwidth")
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 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
SIM-package         11.231  0.160  11.403
integrated.analysis  9.183  0.031   9.226
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/SIM.Rcheck/00check.log’
for details.



Installation output

SIM.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SIM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SIM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c withinWindow.c -o withinWindow.o
clang -mmacosx-version-min=10.13 -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 SIM.so withinWindow.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-SIM/00new/SIM/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 (SIM)

Tests output


Example timings

SIM.Rcheck/SIM-Ex.timings

nameusersystemelapsed
RESOURCERER.annotation.to.ID0.0000.0000.001
SIM-package11.231 0.16011.403
acgh.data0.0020.0010.004
assemble.data0.0470.0090.058
chrom.table0.0020.0020.004
expr.data0.0030.0020.005
getoverlappingregions0.0000.0010.000
impute.nas.by.surrounding000
integrated.analysis9.1830.0319.226
link.metadata000
samples0.0020.0020.003
sim.plot.overlapping.indep.dep.features0.0730.0080.080
sim.plot.pvals.on.genome0.2210.0310.252
sim.plot.pvals.on.region0.0210.0030.025
sim.plot.zoom.in0.6670.0200.688
sim.plot.zscore.heatmap0.4720.0570.531
sim.update.chrom.table0.0000.0000.001
tabulate.pvals0.0070.0010.008
tabulate.top.dep.features0.0210.0040.024
tabulate.top.indep.features0.0140.0020.017