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BioC 3.5: CHECK report for edge on veracruz2

This page was generated on 2017-08-16 13:33:17 -0400 (Wed, 16 Aug 2017).

Package 388/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edge 2.8.0
John D. Storey , Andrew J. Bass
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/edge
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: edge
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edge_2.8.0.tar.gz
StartedAt: 2017-08-16 02:18:23 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:21:38 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 194.6 seconds
RetCode: 0
Status:  OK 
CheckDir: edge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings edge_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/edge.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘edge’ version ‘2.8.0’
* 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 ‘edge’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
build_study: no visible global function definition for ‘as.formula’
createSet: no visible global function definition for ‘model.matrix’
deSetCheck: no visible global function definition for ‘model.matrix’
fitFDist: no visible global function definition for ‘median’
fitFDist: no visible global function definition for ‘lm.fit’
fitFDist: no visible global function definition for ‘predict’
fit_wmodels: no visible global function definition for ‘model.matrix’
fit_wmodels: no visible global function definition for ‘lm.wfit’
null: no visible global function definition for ‘model.matrix’
apply_sva,deSet: no visible global function definition for ‘as.formula’
apply_sva,deSet: no visible global function definition for ‘terms’
fit_models,deSet: no visible global function definition for
  ‘model.matrix’
fullModel<-,deSet: no visible global function definition for
  ‘model.matrix’
lrt,deSet-deFit: no visible global function definition for ‘pf’
nullModel<-,deSet: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  as.formula lm.fit lm.wfit median model.matrix pf predict terms
Consider adding
  importFrom("stats", "as.formula", "lm.fit", "lm.wfit", "median",
             "model.matrix", "pf", "predict", "terms")
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
apply_snm 14.017  1.069  15.505
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/edge.Rcheck/00check.log’
for details.


edge.Rcheck/00install.out:

* installing *source* package ‘edge’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c edge-init.c -o edge-init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c edgeKLODP.c -o edgeKLODP.o
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 edge.so edge-init.o edgeKLODP.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/edge.Rcheck/edge/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 (edge)

edge.Rcheck/edge-Ex.timings:

nameusersystemelapsed
apply_jackstraw2.6550.0422.770
apply_qvalue0.8970.0190.952
apply_snm14.017 1.06915.505
apply_sva3.0490.2263.367
betaCoef0.4010.0060.417
build_models0.4020.0110.440
build_study0.3970.0060.440
deSet0.7270.0080.776
edge000
endotoxin1.2080.0631.320
fitFull0.3220.0050.330
fitNull0.3380.0080.364
fit_models0.6270.0450.695
fullMatrix0.3870.0070.413
fullModel0.5890.0190.632
gibson0.8750.0480.945
individual0.3980.0140.430
kidney1.0660.0761.183
kl_clust0.5290.0170.579
lrt1.1500.0931.311
nullMatrix0.4390.0130.620
nullModel0.9750.0221.040
odp1.7180.2261.986
qvalueObj0.9800.0791.086
resFull0.3380.0050.349
resNull0.3640.0090.383
sType0.3580.0060.392
show0.9030.0841.017
summary1.0010.0861.124