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BioC 3.2: CHECK report for IRanges on linux1.bioconductor.org

This page was generated on 2015-10-27 17:23:31 -0400 (Tue, 27 Oct 2015).

Package 541/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.4.1
Bioconductor Package Maintainer
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/IRanges
Last Changed Rev: 109784 / Revision: 109947
Last Changed Date: 2015-10-20 02:25:43 -0400 (Tue, 20 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.4.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_2.4.1.tar.gz
StartedAt: 2015-10-27 04:57:06 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:59:51 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 164.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_2.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/IRanges.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.4.1’
* 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 ‘IRanges’ can be installed ... [12s/12s] 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
Unexported object imported by a ':::' call: ‘stats:::window.default’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
subsetByOverlaps,RangedData-RangedData : .local: possible error in
  is.na(findOverlaps(ranges(query), ranges(subject), maxgap = maxgap,
  minoverlap = minoverlap, type = match.arg(type), select =
  "arbitrary"), algorithm = match.arg(algorithm)): unused argument
  (algorithm = match.arg(algorithm))
subsetByOverlaps,RangedData-RangesList : .local: possible error in
  is.na(findOverlaps(ranges(query), subject, maxgap = maxgap,
  minoverlap = minoverlap, type = match.arg(type), select =
  "arbitrary"), algorithm = match.arg(algorithm)): unused argument
  (algorithm = match.arg(algorithm))
subsetByOverlaps,RangesList-RangedData : .local: possible error in
  is.na(findOverlaps(query, ranges(subject), maxgap = maxgap,
  minoverlap = minoverlap, type = match.arg(type), select =
  "arbitrary"), algorithm = match.arg(algorithm)): unused argument
  (algorithm = match.arg(algorithm))
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '!' and siglist 'List'
  generic '<=' and siglist 'List,List'
  generic '<=' and siglist 'List,list'
  generic '<=' and siglist 'list,List'
  generic '==' and siglist 'List,List'
  generic '==' and siglist 'List,list'
  generic '==' and siglist 'list,List'
  generic 'all' and siglist 'CompressedAtomicList'
  generic 'any' and siglist 'CompressedAtomicList'
  generic 'anyDuplicated' and siglist 'RangesNSBS'
  generic 'anyDuplicated' and siglist 'RleNSBS'
  generic 'as.integer' and siglist 'RangesNSBS'
  generic 'as.integer' and siglist 'RleNSBS'
  generic 'c' and siglist 'SimpleList'
  generic 'cbind' and siglist 'Rle'
  generic 'cbind' and siglist 'RleList'
  generic 'coerce' and siglist 'Hits,CompressedIntegerList'
  generic 'coerce' and siglist 'Hits,IRanges'
  generic 'coerce' and siglist 'Hits,IntegerList'
  generic 'coerce' and siglist 'Hits,Partitioning'
  generic 'coerce' and siglist 'Hits,PartitioningByEnd'
  generic 'coerce' and siglist 'Hits,Ranges'
  generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
  generic 'coerce' and siglist 'Ranges,RangesList'
  generic 'colnames' and siglist 'SDFLWrapperForTransform'
  generic 'compare' and siglist 'List,List'
  generic 'compare' and siglist 'List,list'
  generic 'compare' and siglist 'list,List'
  generic 'duplicated' and siglist 'List'
  generic 'is.na' and siglist 'CompressedList'
  generic 'is.na' and siglist 'List'
  generic 'length' and siglist 'RangesNSBS'
  generic 'length' and siglist 'RleNSBS'
  generic 'match' and siglist 'CompressedList,list'
  generic 'match' and siglist 'CompressedList,vector'
  generic 'match' and siglist 'List,List'
  generic 'match' and siglist 'List,Vector'
  generic 'match' and siglist 'List,list'
  generic 'match' and siglist 'List,vector'
  generic 'match' and siglist 'list,List'
  generic 'mean' and siglist 'CompressedIntegerList'
  generic 'mean' and siglist 'CompressedLogicalList'
  generic 'mean' and siglist 'CompressedNumericList'
  generic 'overlapsAny' and siglist 'integer,Ranges'
  generic 'paste' and siglist 'CompressedAtomicList'
  generic 'range' and siglist 'CompressedIntegerList'
  generic 'range' and siglist 'CompressedLogicalList'
  generic 'range' and siglist 'CompressedNumericList'
  generic 'relistToClass' and siglist 'Hits'
  generic 'splitAsList' and siglist 'ANY,List'
  generic 'splitAsList' and siglist 'ANY,Rle'
  generic 'splitAsList' and siglist 'ANY,vectorORfactor'
  generic 'unique' and siglist 'List'
  generic 'unique' and siglist 'SimpleList'
  generic 'unlist' and siglist 'SimpleFactorList'
  generic 'unlist' and siglist 'SimpleRleList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘IRanges_unit_tests.R’ [74s/74s]
 [74s/74s] 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/IRanges.Rcheck/00check.log’
for details.


IRanges.Rcheck/00install.out:

* installing *source* package ‘IRanges’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c GappedRanges_class.c -o GappedRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Grouping_class.c -o Grouping_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c IRanges_class.c -o IRanges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c NCList.c -o NCList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c RangedData_class.c -o RangedData_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Ranges_class.c -o Ranges_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Ranges_comparison.c -o Ranges_comparison.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:503:28: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (*out_ranges_are_tiles && x_end != cvg_len)
                            ^
coverage_methods.c:419:21: note: ‘x_end’ was declared here
      i, j, x_start, x_end, shift_elt, tmp;
                     ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function ‘reduce_ranges’:
inter_range_methods.c:168:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Hits","PartitioningByEnd"’: no definition for class “PartitioningByEnd”
in method for ‘coerce’ with signature ‘"Hits","Partitioning"’: no definition for class “Partitioning”
in method for ‘coerce’ with signature ‘"Hits","Ranges"’: no definition for class “Ranges”
in method for ‘coerce’ with signature ‘"Hits","IRanges"’: no definition for class “IRanges”
in method for ‘coerce’ with signature ‘"Hits","CompressedIntegerList"’: no definition for class “CompressedIntegerList”
in method for ‘coerce’ with signature ‘"Hits","IntegerList"’: no definition for class “IntegerList”
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
in method for ‘!’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","list"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","vector"’: no definition for class “CompressedList”
in method for ‘duplicated’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘unique’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘is.na’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)

IRanges.Rcheck/IRanges-Ex.timings:

nameusersystemelapsed
AtomicList-class0.1730.0000.173
CompressedList-class0.0090.0000.009
DataFrame-utils0.1130.0000.113
GappedRanges-class0.0840.0000.085
Grouping-class0.0440.0000.044
Hits-class-leftovers0.040.000.04
IRanges-class1.0770.0201.097
IRanges-constructor0.0200.0040.024
IRanges-utils1.2030.0081.213
IRangesList-class0.0440.0000.044
IntervalForest-class0.0010.0000.001
IntervalTree-class0.0010.0000.001
List-class-leftovers0.0250.0030.030
MaskCollection-class0.1240.0040.128
NCList-class0.0220.0040.025
RDApplyParams-class0.460.000.46
RangedData-class1.0940.0111.107
RangedDataList-class0.0330.0000.033
RangedSelection-class0.0240.0000.024
Ranges-class0.0910.0000.091
Ranges-comparison0.0810.0000.080
RangesList-class0.0770.0000.077
Rle-class-leftovers0.0080.0000.008
RleViews-class0.0790.0000.078
RleViewsList-class0.0580.0000.058
Views-class0.0830.0000.084
ViewsList-class0.0010.0000.001
coverage-methods0.2170.0080.225
expand-methods0.1790.0000.179
extractList0.1130.0030.118
findOverlaps-methods0.2280.0050.233
inter-range-methods0.8430.0000.851
intra-range-methods0.2930.0040.297
mapCoords-methods000
multisplit0.0180.0000.018
nearest-methods0.0480.0000.047
read.Mask0.0440.0000.044
reverse-methods0.1030.0040.107
setops-methods0.1550.0000.155
slice-methods0.0090.0030.013
view-summarization-methods0.0120.0010.012