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BioC 3.6: CHECK report for oligo on malbec1

This page was generated on 2017-08-16 13:17:23 -0400 (Wed, 16 Aug 2017).

Package 928/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.41.1
Benilton Carvalho
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo
Last Changed Rev: 131485 / Revision: 131943
Last Changed Date: 2017-07-21 13:30:23 -0400 (Fri, 21 Jul 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: oligo
Version: 1.41.1
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings oligo_1.41.1.tar.gz
StartedAt: 2017-08-16 01:08:55 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:14:33 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 338.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: oligo.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings oligo_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/oligo.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 ‘oligo/DESCRIPTION’ ... OK
* this is package ‘oligo’ version ‘1.41.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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 ‘oligo’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 29.6Mb
  sub-directories of 1Mb or more:
    doc      12.9Mb
    scripts  15.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘biomaRt’ ‘AnnotationDbi’ ‘GenomeGraphs’ ‘RCurl’ ‘ff’
A package should be listed in only one of these fields.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘oligo’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::annotatedDataFrameFromMatrix’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
  .Call("read_abatch", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
  partial argument match of 'nr' to 'nrow'
image,FeatureSet: warning in matrix(NA, nr = geom[1], nc = geom[2]):
  partial argument match of 'nc' to 'ncol'
NUSE: no visible global function definition for ‘abline’
RLE: no visible global function definition for ‘abline’
basicMvApairsPlot: no visible binding for global variable
  ‘smoothScatter’
basicMvApairsPlot: no visible global function definition for ‘frame’
basicMvApairsPlot: no visible global function definition for ‘text’
basicMvApairsPlot: no visible global function definition for ‘IQR’
basicMvApairsPlot: no visible global function definition for ‘mtext’
basicMvAplot: no visible binding for global variable ‘smoothScatter’
basicMvAplot: no visible global function definition for ‘IQR’
basicMvAplot: no visible global function definition for ‘loess’
basicMvAplot: no visible global function definition for ‘approx’
basicMvAplot: no visible global function definition for ‘abline’
basicMvAplot: no visible global function definition for ‘text’
fitAffySnpMixture: no visible global function definition for
  ‘aggregate’
getRefDABG: no visible global function definition for ‘data’
invariantsetV: no visible global function definition for
  ‘smooth.spline’
invariantsetV: no visible global function definition for ‘approx’
loessNormV: no visible global function definition for ‘loess’
loessNormV: no visible global function definition for ‘predict’
maplot: no visible binding for global variable ‘smoothScatter’
qsplineNorm: no visible global function definition for ‘smooth.spline’
qsplineNorm: no visible global function definition for ‘splinefun’
MAplot,ExpressionSet: no visible binding for global variable
  ‘smoothScatter’
MAplot,FeatureSet: no visible binding for global variable
  ‘smoothScatter’
MAplot,TilingFeatureSet: no visible binding for global variable
  ‘smoothScatter’
MAplot,TilingFeatureSet: no visible global function definition for
  ‘rnorm’
MAplot,matrix: no visible binding for global variable ‘smoothScatter’
backgroundCorrect,matrix: no visible binding for global variable
  ‘intensities’
pmFragmentLength,AffySNPPDInfo: no visible global function definition
  for ‘complete.cases’
pmindex,GenericPDInfo: no visible binding for global variable
  ‘man_fsetid’
Undefined global functions or variables:
  IQR abline aggregate approx complete.cases data frame intensities
  loess man_fsetid mtext predict rnorm smooth.spline smoothScatter
  splinefun text
Consider adding
  importFrom("graphics", "abline", "frame", "mtext", "smoothScatter",
             "text")
  importFrom("stats", "IQR", "aggregate", "approx", "complete.cases",
             "loess", "predict", "rnorm", "smooth.spline", "splinefun")
  importFrom("utils", "data")
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 ... WARNING
Codoc mismatches from documentation object 'boxplot':
\S4method{boxplot}{FeatureSet}
  Code: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
                 = log2, nsample = 10000, target = "mps1", ...)
  Docs: function(x, which = c("pm", "mm", "bg", "both", "all"), transfo
                 = log2, nsample = 10000, ...)
  Argument names in code not in docs:
    target
  Mismatches in argument names:
    Position: 5 Code: target Docs: ...

Codoc mismatches from documentation object 'hist':
\S4method{hist}{FeatureSet}
  Code: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
                 "all"), nsample = 10000, target = "mps1", ...)
  Docs: function(x, transfo = log2, which = c("pm", "mm", "bg", "both",
                 "all"), nsample = 10000, ...)
  Argument names in code not in docs:
    target
  Mismatches in argument names:
    Position: 5 Code: target Docs: ...

S4 class codoc mismatches from documentation object 'oligoPLM-class':
Slots for class 'oligoPLM'
  Code: annotation chip.coefs description geometry manufacturer method
        narrays nprobes nprobesets phenoData probe.coefs protocolData
        residualSE residuals se.chip.coefs se.probe.coefs weights
  Docs: annotation chip.coefs geometry manufacturer method narrays
        nprobes nprobesets probe.coefs residualSE residuals
        se.chip.coefs se.probe.coefs weights

* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘Makefile’
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
preprocessTools 25.236  0.032  25.347
getProbeInfo    11.476  0.324  11.940
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.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, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/oligo.Rcheck/00check.log’
for details.


oligo.Rcheck/00install.out:

* installing *source* package ‘oligo’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function ‘gzcountLines’:
ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types]
   while (!gzeof(file)){
                 ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1475:21: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzeof OF((gzFile file));
                     ^
ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
     gzgets(file, buffer, 1000);
            ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1372:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                        ^
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:46:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   fp = gzopen(currentFile, "rb");
      ^
ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzgets(fp, buffer, LINEMAX);
          ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1372:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                        ^
ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(fp);
           ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:134:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
      ^
ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(fp);
           ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:145:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer, LINEMAX, fp);
   ^
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:320:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer, LINEMAX, fp);
   ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.6-bioc/R/lib -lRblas -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/oligo.Rcheck/oligo/libs
** R
** inst
** preparing package for lazy loading
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligo)

oligo.Rcheck/oligo-Ex.timings:

nameusersystemelapsed
Index-methods000
IntensityMatrix-methods1.2040.0161.388
MAplot-methods1.8480.0121.890
basecontent000
basicPLM2.7840.0002.786
basicRMA2.7160.0002.718
colors0.0320.0000.031
coordinates000
fitProbeLevelModel4.4840.0364.582
getProbeInfo11.476 0.32411.940
image0.8400.0160.857
justSNPRMA0.0040.0000.000
list.xysfiles000
oligoPLM-class0.0000.0000.001
paCalls000
preprocessTools25.236 0.03225.347
read.celfiles4.1160.0564.261
read.xysfiles0.5480.0000.551
rma-methods2.0360.0042.047
sequenceDesignMatrix0.0080.0000.010