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BioC 3.4: CHECK report for snapCGH on morelia

This page was generated on 2017-04-15 16:22:13 -0400 (Sat, 15 Apr 2017).

Package 1163/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.44.0
John Marioni
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/snapCGH
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: snapCGH
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings snapCGH_1.44.0.tar.gz
StartedAt: 2017-04-15 08:17:27 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 08:20:06 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 158.9 seconds
RetCode: 0
Status:  OK 
CheckDir: snapCGH.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings snapCGH_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/snapCGH.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snapCGH/DESCRIPTION’ ... OK
* this is package ‘snapCGH’ version ‘1.44.0’
* 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 ‘snapCGH’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘DNAcopy’ ‘limma’ ‘methods’
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 ... 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
MergeLevels.new: warning in matrix(1:ncol(dst), nrow = nrow(dst), ncol
  = ncol(dst), b = TRUE): partial argument match of 'b' to 'byrow'
Viterbi.five: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
Viterbi.four: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
Viterbi.three: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
Viterbi.two: warning in matrix(nrow = K, ncol = n, b = TRUE): partial
  argument match of 'b' to 'byrow'
find.param.five: warning in matrix(c(1 - p1 - p2 - p3 - p4, p1, p2, p3,
  p4, p5, 1 - p5 - p6 - p7 - p8, p6, p7, p8, p9, p10, 1 - p9 - p10 -
  p11 - p12, p11, p12, p13, p14, p15, 1 - p13 - p14 - p15 - p16, p16,
  p17, p18, p19, p20, 1 - p17 - p18 - p19 - p20), ncol = 5, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.five: warning in matrix(c(p1 + p2 + p3 + p4, -p1, -p2, -p3,
  -p4, -p5, p5 + p6 + p7 + p8, -p6, -p7, -p8, -p9, -p10, p9 + p10 + p11
  + p12, -p11, -p12, -p13, -p14, -p15, p13 + p14 + p15 + p16, -p16,
  -p17, -p18, -p19, -p20, p17 + p18 + p19 + p20), ncol = 5, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.four: warning in matrix(c(abs(1 - p1 - p2 - p3), p1, p2, p3,
  p4, abs(1 - p4 - p5 - p6), p5, p6, p7, p8, abs(1 - p7 - p8 - p9), p9,
  p10, p11, p12, abs(1 - p10 - p11 - p12)), ncol = 4, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.four: warning in matrix(c(p1 + p2 + p3, -p1, -p2, -p3, -p4,
  p4 + p5 + p6, -p5, -p6, -p7, -p8, p7 + p8 + p9, -p9, -p10, -p11,
  -p12, p10 + p11 + p12), ncol = 4, b = TRUE): partial argument match
  of 'b' to 'byrow'
find.param.three: warning in matrix(c(abs(1 - p1 - p2), p1, p2, p3,
  abs(1 - p3 - p4), p4, p5, p6, abs(1 - p5 - p6)), ncol = 3, b = TRUE):
  partial argument match of 'b' to 'byrow'
find.param.three: warning in matrix(c(p1 + p2, -p1, -p2, -p3, p3 + p4,
  -p4, -p5, -p6, p5 + p6), ncol = 3, b = TRUE): partial argument match
  of 'b' to 'byrow'
find.param.two: warning in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2,
  b = TRUE): partial argument match of 'b' to 'byrow'
find.param.two: warning in matrix(c(p1, -p1, -p2, p2), ncol = 2, b =
  TRUE): partial argument match of 'b' to 'byrow'
genomePlot: warning in matrix(data[ord, ], nrow =
  nrow(as.matrix(data[ord, ])), ncol = ncol(data), b = FALSE, dimnames
  = dimnames(data)): partial argument match of 'b' to 'byrow'
genomePlot: warning in matrix(data[chrom == nchr, ], nrow =
  nrow(as.matrix(data[chrom == nchr, ])), ncol = ncol(data), b = FALSE,
  dimnames = dimnames(data[chrom == nchr, ])): partial argument match
  of 'b' to 'byrow'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.non.tiled' to
  'zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.non.tiled' to
  'non.zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.tiled' to
  'zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.short[[i]],
  short.tiled[i], length.short.tiled[i], end.pos.short[[i]],
  start.short.tiled[i], length.chrom.short[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.tiled' to
  'non.zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.non.tiled' to
  'zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.non.tiled' to
  'non.zero.length.distr.non.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'zero.length.distr.tiled' to
  'zero.length.distr.tiled.'
simulateData: warning in generate.data(mid.point.long[[i]],
  long.tiled[i], length.long.tiled[i], end.pos.long[[i]],
  start.long.tiled[i], length.chrom.long[i],
  zero.length.distr.non.tiled = zero.length.distr.non.tiled,
  non.zero.length.distr.non.tiled = non.zero.length.distr.non.tiled,
  zero.length.distr.tiled = zero.length.distr.tiled,
  non.zero.length.distr.tiled = non.zero.length.distr.tiled): partial
  argument match of 'non.zero.length.distr.tiled' to
  'non.zero.length.distr.tiled.'
generate.data: no visible binding for global variable
  ‘zero.length.distr.non.tiled’
generate.data: no visible binding for global variable
  ‘non.zero.length.distr.non.tiled’
generate.data: no visible binding for global variable
  ‘zero.length.distr.tiled’
generate.data: no visible binding for global variable
  ‘non.zero.length.distr.tiled’
heatmapGenome: no visible binding for global variable ‘floor.func’
readPositionalInfo: no visible binding for global variable ‘RGList’
simulateData: no visible binding for global variable
  ‘zero.length.distr.non.tiled’
simulateData: no visible binding for global variable
  ‘zero.length.distr.tiled’
simulateData: no visible binding for global variable
  ‘non.zero.length.distr.non.tiled’
simulateData: no visible binding for global variable
  ‘non.zero.length.distr.tiled’
Undefined global functions or variables:
  RGList floor.func non.zero.length.distr.non.tiled
  non.zero.length.distr.tiled zero.length.distr.non.tiled
  zero.length.distr.tiled
* checking Rd files ... NOTE
prepare_Rd: genomePlot.Rd:51-57: Dropping empty section \examples
prepare_Rd: heatmapGenome.Rd:76-77: Dropping empty section \examples
prepare_Rd: plotSegmentedGenome.Rd:52-58: Dropping empty section \examples
prepare_Rd: sim.structure.Rd:57-58: Dropping empty section \examples
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/snapCGH.Rcheck/00check.log’
for details.


snapCGH.Rcheck/00install.out:

* installing *source* package ‘snapCGH’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c optimizer.c -o optimizer.o
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                    ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                    ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                    ^
15 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/snapCGH.Rcheck/snapCGH/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 (snapCGH)

snapCGH.Rcheck/snapCGH-Ex.timings:

nameusersystemelapsed
LargeDataObject000
convert.output0.0040.0000.005
dim0.0050.0000.005