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BioC 3.5: CHECK report for CSSP on malbec2

This page was generated on 2017-08-16 13:15:09 -0400 (Wed, 16 Aug 2017).

Package 301/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSSP 1.14.0
Chandler Zuo
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/CSSP
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: CSSP
Version: 1.14.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CSSP_1.14.0.tar.gz
StartedAt: 2017-08-15 22:18:57 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:19:47 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 49.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CSSP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CSSP_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CSSP.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CSSP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSSP’ version ‘1.14.0’
* 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 ‘CSSP’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’ ‘utils’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.allFit: no visible global function definition for ‘quantile’
.allFit: no visible global function definition for ‘model.matrix’
.allFit: no visible global function definition for ‘glm’
.csspfit : pval.nb.cont.trunc: no visible global function definition
  for ‘runif’
.csspfit : pval.nb.cont.trunc: no visible global function definition
  for ‘pnbinom’
.csspfit : pval.nb.cont: no visible global function definition for
  ‘runif’
.csspfit : pval.nb.cont: no visible global function definition for
  ‘pnbinom’
.csspfit : pval.mod.w: no visible global function definition for
  ‘dnbinom’
.csspfit: no visible global function definition for ‘pnbinom’
.csspfit: no visible global function definition for ‘dnbinom’
.csspfit: no visible global function definition for ‘weighted.mean’
.csspfit: no visible global function definition for ‘na.omit’
.csspfit: no visible global function definition for ‘new’
.gridFit: no visible global function definition for ‘quantile’
.gridFit: no visible global function definition for ‘model.matrix’
.gridFit: no visible global function definition for ‘glm’
.gridFit: no visible global function definition for ‘predict.glm’
.nonpaFit: no visible global function definition for ‘quantile’
.nonpaFit: no visible global function definition for ‘weighted.mean’
createBinData: no visible global function definition for ‘read.table’
createBinData: no visible global function definition for ‘new’
createBinData: no visible global function definition for ‘na.omit’
readBinFile: no visible global function definition for ‘read.table’
callpeak,CSSPFit: no visible global function definition for ‘pnbinom’
callpeak,CSSPFit: no visible global function definition for ‘pgamma’
cssp.power,CSSPFit: no visible global function definition for ‘rgamma’
cssp.power,CSSPFit: no visible global function definition for ‘rbinom’
cssp.power,CSSPFit: no visible global function definition for ‘rpois’
cssp.power,CSSPFit: no visible global function definition for ‘pnbinom’
cssp.power,CSSPFit: no visible global function definition for ‘na.omit’
cssp.power,CSSPFit: no visible global function definition for ‘pgamma’
cssp.power,CSSPFit: no visible global function definition for ‘qnbinom’
cssp.power,CSSPFit: no visible global function definition for ‘qgamma’
cssp.power,CSSPFit: no visible global function definition for ‘runif’
cssp.power,CSSPFit: no visible global function definition for
  ‘weighted.mean’
cssp.sim,CSSPFit: no visible global function definition for ‘rgamma’
cssp.sim,CSSPFit: no visible global function definition for ‘rbinom’
cssp.sim,CSSPFit: no visible global function definition for ‘runif’
fit.freq,CSSPFit: no visible global function definition for ‘quantile’
fit.freq,CSSPFit : <anonymous>: no visible global function definition
  for ‘dnbinom’
pBBT,CSSPFit: no visible global function definition for ‘pgamma’
qBBT,CSSPFit: no visible global function definition for ‘quantile’
qBBT,CSSPFit: no visible global function definition for ‘uniroot’
show,CSSPFit: no visible global function definition for ‘showClass’
Undefined global functions or variables:
  dnbinom glm model.matrix na.omit new pgamma pnbinom predict.glm
  qgamma qnbinom quantile rbinom read.table rgamma rpois runif
  showClass uniroot weighted.mean
Consider adding
  importFrom("methods", "new", "showClass")
  importFrom("stats", "dnbinom", "glm", "model.matrix", "na.omit",
             "pgamma", "pnbinom", "predict.glm", "qgamma", "qnbinom",
             "quantile", "rbinom", "rgamma", "rpois", "runif", "uniroot",
             "weighted.mean")
  importFrom("utils", "read.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
File ‘CSSP/libs/CSSP.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gridSample.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gridSample.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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
cssp.power-methods 19.564  0.028  19.603
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_tests.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/CSSP.Rcheck/00check.log’
for details.


CSSP.Rcheck/00install.out:

* installing *source* package ‘CSSP’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bincount.c -o bincount.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c binpower.c -o binpower.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c gridLogMean.c -o gridLogMean.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c gridMGC.c -o gridMGC.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c gridMean.c -o gridMean.o
gridMean.c: In function ‘gridMGCmean_c’:
gridMean.c:10:63: warning: unused variable ‘counter’ [-Wunused-variable]
   R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
                                                               ^
gridMean.c: In function ‘gridMmean_c’:
gridMean.c:177:63: warning: unused variable ‘counter’ [-Wunused-variable]
   R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
                                                               ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c gridMode.c -o gridMode.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c gridNonpa.c -o gridNonpa.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c gridSample.c -o gridSample.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c tag2bin.c -o tag2bin.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o CSSP.so bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/CSSP.Rcheck/CSSP/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CSSP)

CSSP.Rcheck/CSSP-Ex.timings:

nameusersystemelapsed
CSSPFit-class0.0000.0000.002
bindcount0.1200.0040.127
bindcount.chr0.020.000.02
callpeak-methods0.0080.0040.011
createBinData0.3640.0000.366
cssp.fit-methods3.7120.0043.717
cssp.power-methods19.564 0.02819.603
cssp.sim-methods0.0160.0000.017
fit.freq-methods0.1880.0000.189
pBBT-methods0.0040.0000.004
peakcount0.1040.0000.102
peakcount.chr0.0160.0000.014
qBBT-methods0.0320.0000.032
readBinFile0.0040.0040.009
tag2bin0.0080.0000.008
tag2bin.chr0.0040.0000.006