Package: waveTiling

Version: 1.28.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:waveTiling.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings waveTiling_1.28.0.tar.gz

StartedAt: 2020-04-15 01:23:47 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:29:16 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 329.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: waveTiling.Rcheck

Warnings: 1

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:waveTiling.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings waveTiling_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/waveTiling.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waveTiling/DESCRIPTION’ ... OK
* this is package ‘waveTiling’ version ‘1.28.0’
* 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 ‘waveTiling’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GenomeGraphs' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.10-bioc/meat/waveTiling.Rcheck/00install.out’ for details.
* 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
Package in Depends field not imported from: ‘GenomeGraphs’
  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 ... NOTE
Foreign function calls to a different package:
  .C("dwt", ..., PACKAGE = "waveslim")
  .C("idwt", ..., PACKAGE = "waveslim")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[1]]), end(regions[[1]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[2]]), end(regions[[2]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[effectId[effectNo] + 1]]),
  end(regions[[effectId[effectNo] + 1]]))), location = Gloc, start =
  sta, end = end, region = c(trackCount, trackCount), dp =
  DisplayPars(color = "darkgrey", alpha = 0.1)): partial argument match
  of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[effectId[length(effectsToPlot) -
  2] + 2]]), end(regions[[effectId[length(effectsToPlot) - 2] + 2]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[i + 1]]), end(regions[[i +
  1]]))), location = Gloc, start = sta, end = end, region =
  c(trackCount, trackCount), dp = DisplayPars(color = "darkgrey", alpha
  = 0.1)): partial argument match of 'location' to 'locations'
plotWfm,WfmFit-WfmInf: warning in
  makeNewTranscriptRectangleOverlay(sigRegions =
  as.matrix(data.frame(start(regions[[i]]), end(regions[[i]]))),
  location = Gloc, start = sta, end = end, region = c(trackCount,
  trackCount), dp = DisplayPars(color = "darkgrey", alpha = 0.1)):
  partial argument match of 'location' to 'locations'
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘DisplayPars’
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘transcripts’
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘elementMetadata’
makeNewAnnotationTextOverlay: no visible global function definition for
  ‘makeTextOverlay’
makeNewAnnotationTrack: no visible global function definition for
  ‘DisplayPars’
makeNewAnnotationTrack: no visible global function definition for
  ‘exons’
makeNewAnnotationTrack: no visible global function definition for
  ‘elementMetadata’
makeNewAnnotationTrack: no visible global function definition for
  ‘makeAnnotationTrack’
makeNewTranscriptRectangleOverlay: no visible global function
  definition for ‘DisplayPars’
makeNewTranscriptRectangleOverlay: no visible global function
  definition for ‘makeRectangleOverlay’
pm2mm: no visible global function definition for ‘subseq’
filterOverlap,WaveTilingFeatureSet: no visible global function
  definition for ‘ac.character’
filterOverlap,WaveTilingFeatureSet: no visible binding for global
  variable ‘dataMMSegRevComp’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
  definition for ‘exons’
getNonAnnotatedRegions,WfmFit-WfmInf: no visible global function
  definition for ‘Rle’
getSigGenes,WfmFit-WfmInf: no visible global function definition for
  ‘transcripts’
getSigGenes,WfmFit-WfmInf: no visible global function definition for
  ‘queryHits’
getSigGenes,WfmFit-WfmInf: no visible global function definition for
  ‘subjectHits’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘makeGenericArray’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘DisplayPars’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘makeGenomeAxis’
plotWfm,WfmFit-WfmInf: no visible global function definition for
  ‘gdPlot’
Undefined global functions or variables:
  DisplayPars Rle ac.character dataMMSegRevComp elementMetadata exons
  gdPlot makeAnnotationTrack makeGenericArray makeGenomeAxis
  makeRectangleOverlay makeTextOverlay queryHits subjectHits subseq
  transcripts
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
wfm.fit                       31.392  0.640  32.083
WaveTilingFeatureSet-class    30.632  0.704  31.649
selectProbesFromFilterOverlap 12.464  0.236  12.734
MapFilterProbe-class          11.944  0.136  12.156
getNonAnnotatedRegions         5.404  0.296   6.250
getSigGenes                    5.336  0.052   5.480
* 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/waveTiling.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL waveTiling
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘waveTiling’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c waveTiling.c -o waveTiling.o
waveTiling.c: In function ‘MAPMARG’:
waveTiling.c:10:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function ‘MAPMARGEQSMOOTH’:
waveTiling.c:43:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function ‘MAPMARGIMP’:
waveTiling.c:81:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
waveTiling.c: In function ‘MAPMARGIMPEQSMOOTH’:
waveTiling.c:114:11: warning: unused variable ‘n’ [-Wunused-variable]
 int i,j,m,n,Jcount=0;
           ^
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o waveTiling.so waveTiling.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-waveTiling/00new/waveTiling/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
Warning message:
Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path
* DONE (waveTiling)

name	user	system	elapsed
GenomeInfo-class	0.000	0.000	0.001
MapFilterProbe-class	11.944	0.136	12.156
WaveTilingFeatureSet-class	30.632	0.704	31.649
WfmFit-class	1.064	0.048	1.321
WfmFitCircadian-class	0.000	0.000	0.001
WfmFitCustom-class	0.000	0.004	0.001
WfmFitFactor-class	0.000	0.000	0.001
WfmFitTime-class	0.004	0.000	0.001
WfmInf-class	0.812	0.048	0.874
WfmInfCompare-class	0	0	0
WfmInfCustom-class	0	0	0
WfmInfEffects-class	0	0	0
WfmInfMeans-class	0	0	0
WfmInfOverallMean-class	0	0	0
addPheno	0.000	0.000	0.001
bgCorrQn	0	0	0
cel2TilingFeatureSet	0	0	0
filterOverlap	0.000	0.000	0.001
getNonAnnotatedRegions	5.404	0.296	6.250
getSigGenes	5.336	0.052	5.480
makeContrasts	0.004	0.000	0.000
makeDesign	0.004	0.000	0.007
plotWfm	3.408	0.040	3.470
selectProbesFromFilterOverlap	12.464	0.236	12.734
selectProbesFromTilingFeatureSet	0	0	0
wfm.fit	31.392	0.640	32.083
wfm.inference	1.752	0.080	1.832