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BioC 3.4: CHECK report for IRanges on malbec1

This page was generated on 2017-04-15 16:08:49 -0400 (Sat, 15 Apr 2017).

Package 645/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.8.2
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/IRanges
Last Changed Rev: 127452 / Revision: 128728
Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.8.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_2.8.2.tar.gz
StartedAt: 2017-04-14 23:23:12 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:25:54 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 161.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: IRanges.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IRanges_2.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/IRanges.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.8.2’
* package encoding: UTF-8
* 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setCompressedListSummaryMethod : <anonymous>: no visible binding for
  global variable ‘C_fun’
setCompressedListWhichSummaryMethod : def: no visible binding for
  global variable ‘C_fun’
Undefined global functions or variables:
  C_fun
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘%poutside%’ ‘%pover%’ ‘%pwithin%’ ‘diff.IntegerList’
  ‘diff.NumericList’ ‘diff.RleList’ ‘slidingIRanges’ ‘slidingViews’
Undocumented S4 methods:
  generic 'anyDuplicated' and siglist 'RangesNSBS'
  generic 'c' and siglist 'SimpleList'
  generic 'cbind' and siglist 'Rle'
  generic 'cbind' and siglist 'RleList'
  generic 'coerce' and siglist 'AtomicList,RleViews'
  generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
  generic 'coerce' and siglist 'factor,ManyToOneGrouping'
  generic 'colnames' and siglist 'SDFLWrapperForTransform'
  generic 'ifelse' and siglist 'ANY,ANY,List'
  generic 'ifelse' and siglist 'ANY,List,ANY'
  generic 'ifelse' and siglist 'ANY,List,List'
  generic 'ifelse' and siglist 'CompressedLogicalList,ANY,ANY'
  generic 'ifelse' and siglist 'CompressedLogicalList,ANY,List'
  generic 'ifelse' and siglist 'CompressedLogicalList,List,ANY'
  generic 'ifelse' and siglist 'CompressedLogicalList,List,List'
  generic 'ifelse' and siglist 'SimpleLogicalList,ANY,ANY'
  generic 'ifelse' and siglist 'SimpleLogicalList,ANY,List'
  generic 'ifelse' and siglist 'SimpleLogicalList,List,ANY'
  generic 'ifelse' and siglist 'SimpleLogicalList,List,List'
  generic 'length' and siglist 'RangesNSBS'
  generic 'pcompareRecursively' and siglist 'Ranges'
  generic 'relist' and siglist 'grouping,missing'
  generic 'show' and siglist 'RangedDataList'
  generic 'showAsCell' and siglist 'Views'
  generic 'splitAsList' and siglist 'ANY'
  generic 'stack' and siglist 'matrix'
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 ... WARNING
Documented arguments not in \usage in documentation object 'nearest-methods':
  ‘hits’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/IRanges.Rcheck/00check.log’
for details.


IRanges.Rcheck/00install.out:

* installing *source* package ‘IRanges’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Grouping_class.c -o Grouping_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c IRanges_class.c -o IRanges_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c NCList.c -o NCList.o
NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^
NCList.c:1184:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
 static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
             ^
NCList.c: In function ‘NCList_find_overlaps_in_groups’:
NCList.c:1553:7: warning: ‘ans’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Ranges_class.c -o Ranges_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c Ranges_comparison.c -o Ranges_comparison.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include"   -fpic  -g -O2  -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-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 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-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:165:5: warning: ‘revmap_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(revmap_elt,
     ^
inter_range_methods.c:154:11: warning: ‘delta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
inter_range_methods.c:154:11: warning: ‘gapwidth’ may be used uninitialized in this function [-Wmaybe-uninitialized]
inter_range_methods.c:156:14: warning: ‘max_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    width_inc = end_j - max_end;
              ^
inter_range_methods.c:131:6: warning: ‘append_or_drop’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (append_or_drop) {
      ^
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/IRanges.Rcheck/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘ifelse’ from package ‘base’ 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 ‘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-class0.2400.0040.243
AtomicList-utils0.0280.0120.042
CompressedList-class0.0080.0000.010
DataFrame-utils0.1000.0000.099
Grouping-class0.0520.0000.053
Hits-class-leftovers0.0360.0040.039
IRanges-class0.9880.0120.999
IRanges-constructor0.0280.0000.028
IRanges-utils0.8520.0040.855
IRangesList-class0.0280.0000.028
List-class-leftovers0.0160.0000.016
MaskCollection-class0.0520.0120.067
NCList-class0.0160.0000.020
RangedData-class0.6400.0040.647
RangedSelection-class0.0120.0000.014
Ranges-class0.0320.0000.030
Ranges-comparison0.0480.0000.047
RangesList-class0.0600.0000.059
Rle-class-leftovers0.0040.0000.004
RleViews-class0.0440.0000.042
RleViewsList-class0.0320.0000.030
Views-class0.0240.0000.026
ViewsList-class0.0040.0000.001
bind-arrays0.0080.0000.010
coverage-methods0.1240.0000.122
extractList0.0480.0000.048
findOverlaps-methods0.1800.0000.178
inter-range-methods0.5520.0000.551
intra-range-methods0.1640.0000.164
multisplit0.0160.0000.014
nearest-methods0.0320.0000.032
read.Mask0.0240.0040.029
reverse-methods0.0400.0000.037
setops-methods0.1120.0000.113
slice-methods0.0080.0000.009
view-summarization-methods0.0120.0000.012