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Package 219/671HostnameOS / ArchBUILDCHECKBUILD BIN
flagme 1.16.1
Mark Robinson
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/flagme
Last Changed Rev: 75695 / Revision: 76155
Last Changed Date: 2013-04-16 05:37:24 -0700 (Tue, 16 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: flagme
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flagme_1.16.1.tar.gz
StartedAt: 2013-05-01 05:11:58 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 05:14:42 -0700 (Wed, 01 May 2013)
EllapsedTime: 164.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flagme.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flagme.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flagme/DESCRIPTION' ... OK
* this is package 'flagme' version '1.16.1'
* 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 'flagme' can be installed ... [10s/12s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 line endings 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 examples ... [52s/55s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
parseChromaTOF 8.071  0.058   8.407
parseELU       6.695  0.088   7.846
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

flagme.Rcheck/00install.out:

* installing *source* package 'flagme' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c dp.c -o dp.o
dp.c:19:27: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, ind, nc1 = *nc1_, nc2=*nc2_, df=*df_, w=*w_, n=(w-1)/2;
                    ˜˜˜   ^˜˜˜˜
dp.c:19:38: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, ind, nc1 = *nc1_, nc2=*nc2_, df=*df_, w=*w_, n=(w-1)/2;
                                 ˜˜˜ ^˜˜˜˜
dp.c:19:48: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, ind, nc1 = *nc1_, nc2=*nc2_, df=*df_, w=*w_, n=(w-1)/2;
                                            ˜˜ ^˜˜˜
dp.c:19:56: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, ind, nc1 = *nc1_, nc2=*nc2_, df=*df_, w=*w_, n=(w-1)/2;
                                                     ˜ ^˜˜
dp.c:70:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  x1sq = (double *) R_alloc(nc1, sizeof(double));
                    ˜˜˜˜˜˜˜ ^˜˜
dp.c:71:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  x2sq = (double *) R_alloc(nc2, sizeof(double));
                    ˜˜˜˜˜˜˜ ^˜˜
dp.c:54:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                            ˜˜   ^˜˜˜
dp.c:54:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                                       ˜˜˜   ^˜˜˜˜
dp.c:54:57: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                                                    ˜˜˜ ^˜˜˜˜
dp.c:54:67: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                                                               ˜˜ ^˜˜˜
dp.c:121:20: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, n = *n_, count=0;
               ˜   ^˜˜
dp.c:168:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  x1sq = (double *) R_alloc(nc1, sizeof(double));
                    ˜˜˜˜˜˜˜ ^˜˜
dp.c:169:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  x2sq = (double *) R_alloc(nc2, sizeof(double));
                    ˜˜˜˜˜˜˜ ^˜˜
dp.c:161:34: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                            ˜˜   ^˜˜˜
dp.c:161:46: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                                       ˜˜˜   ^˜˜˜˜
dp.c:161:57: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                                                    ˜˜˜ ^˜˜˜˜
dp.c:161:67: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i, j, k, hi, lo, ind, nr = *nr_, nc1 = *nc1_, nc2=*nc2_, df=*df_;
                                                               ˜˜ ^˜˜˜
dp.c:217:15: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0;
           ˜˜ ^˜˜˜
dp.c:217:24: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
  int i,j, nr=*nr_, nc=*nc_, tb, count=0, done=0;
                    ˜˜ ^˜˜˜
19 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c init.c -o init.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o flagme.so dp.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'flagme'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flagme)

flagme.Rcheck/flagme-Ex.timings:

nameusersystemelapsed
addAMDISPeaks1.6150.1151.916
addChromaTOFPeaks0.5370.0650.697
betweenAlignment0.0060.0130.019
calcTimeDiffs2.1360.2072.496
clusterAlignment1.9960.1802.180
compress2.4010.1842.627
dp2.3170.1832.571
gatherInfo2.6600.1722.965
imputePeaks3.6000.2393.947
multipleAlignment2.4430.1822.726
normDotProduct2.2580.1752.481
parseChromaTOF8.0710.0588.407
parseELU6.6950.0887.846
peaksAlignment0.0070.0080.015
peaksDataset0.7970.1410.952
plot1.6280.2061.910
plotImage0.4880.1050.620
progressiveAlignment2.5350.1852.784
rmaFitUnit2.0470.1952.437