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BioC 3.0: CHECK report for COMPASS on perceval

This page was generated on 2015-04-10 09:59:16 -0700 (Fri, 10 Apr 2015).

Package 189/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.4.0
Greg Finak
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/COMPASS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: COMPASS
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COMPASS_1.4.0.tar.gz
StartedAt: 2015-04-10 00:12:15 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:16:38 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 262.9 seconds
RetCode: 0
Status:  OK 
CheckDir: COMPASS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COMPASS_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/COMPASS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COMPASS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COMPASS’ version ‘1.4.0’
* 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 ‘COMPASS’ can be installed ... [11s/38s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘devtools’ ‘flowWorkspace’ ‘shiny’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
COMPASSContainerFromGatingSet: no visible global function definition
  for ‘pData’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous> :
  <anonymous>: no visible global function definition for ‘parameters’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for ‘parameters’
COMPASSContainerFromGatingSet : .checkMarkerConsistency : <anonymous>:
  no visible global function definition for ‘getData’
COMPASSContainerFromGatingSet: no visible global function definition
  for ‘parameters’
COMPASSContainerFromGatingSet: no visible global function definition
  for ‘getSingleCellExpression’
draw_polar_legend: no visible binding for global variable ‘trtLabels’
GetThresholdedIntensities: no visible global function definition for
  ‘parameters’
GetThresholdedIntensities: no visible global function definition for
  ‘exprs’
GetThresholdedIntensities : <anonymous>: no visible global function
  definition for ‘getData’
shinyCOMPASS: no visible global function definition for ‘runApp’
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/121s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GetThresholdedIntensities 6.547  0.224  11.706
pheatmap                  1.988  0.031   5.636
shinyCOMPASSDeps          0.923  0.629  95.072
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [4s/6s]
 [5s/8s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/COMPASS.Rcheck/00check.log’
for details.

COMPASS.Rcheck/00install.out:

* installing *source* package ‘COMPASS’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c COMPASS_c.c -o COMPASS_c.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c COMPASS_cpp.cpp -o COMPASS_cpp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c COMPASS_init.c -o COMPASS_init.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o COMPASS.so COMPASS_c.o COMPASS_cpp.o COMPASS_init.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/COMPASS.Rcheck/COMPASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (COMPASS)

COMPASS.Rcheck/COMPASS-Ex.timings:

nameusersystemelapsed
COMPASS0.4230.0220.665
COMPASSContainer0.0520.0010.054
COMPASSContainerFromGatingSet0.0010.0000.001
CellCounts0.9600.0421.267
Combinations0.0010.0000.001
FunctionalityScore0.0060.0030.009
GetThresholdedIntensities 6.547 0.22411.706
PolyfunctionalityScore0.0010.0000.039
Posterior0.0040.0020.054
SimpleCOMPASS0.0020.0010.002
TotalCellCounts0.0300.0010.031
UniqueCombinations0.0070.0010.050
merge.COMPASSContainer0.0210.0020.023
pheatmap1.9880.0315.636
plot.COMPASSResult0.2030.0050.805
print.COMPASSContainer0.0010.0000.002
print.COMPASSResult0.0010.0000.001
shinyCOMPASS0.0020.0000.002
shinyCOMPASSDeps 0.923 0.62995.072
subset.COMPASSContainer0.0020.0000.002
summary.COMPASSContainer0.0050.0010.108
summary.COMPASSResult0.0000.0000.001
transpose_list0.0010.0000.001