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BioC 3.2: CHECK report for gdsfmt on perceval

This page was generated on 2015-08-24 10:54:23 -0700 (Mon, 24 Aug 2015).

Package 381/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.5.12
Xiuwen Zheng
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gdsfmt
Last Changed Rev: 107676 / Revision: 107696
Last Changed Date: 2015-08-21 14:45:13 -0700 (Fri, 21 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ ERROR ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gdsfmt
Version: 1.5.12
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gdsfmt_1.5.12.tar.gz
StartedAt: 2015-08-24 00:53:46 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:00:43 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 417.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: gdsfmt.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gdsfmt_1.5.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.5.12’
* 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 ‘gdsfmt’ can be installed ... [66s/67s] 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 ... 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 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’ ... OK
* checking examples ... ERROR
Running examples in ‘gdsfmt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterApply.gdsn
> ### Title: Apply functions over matrix margins in parallel
> ### Aliases: clusterApply.gdsn
> ### Keywords: GDS utilities
> 
> ### ** Examples
> 
> ###########################################################
> # prepare a GDS file
> 
> # cteate a GDS file
> f <- createfn.gds("test1.gds")
> 
> (n <- add.gdsn(f, "matrix", val=matrix(1:(10*6), nrow=10)))
+ matrix   { Int32 10x6, 240 bytes }
> read.gdsn(index.gdsn(f, "matrix"))
      [,1] [,2] [,3] [,4] [,5] [,6]
 [1,]    1   11   21   31   41   51
 [2,]    2   12   22   32   42   52
 [3,]    3   13   23   33   43   53
 [4,]    4   14   24   34   44   54
 [5,]    5   15   25   35   45   55
 [6,]    6   16   26   36   46   56
 [7,]    7   17   27   37   47   57
 [8,]    8   18   28   38   48   58
 [9,]    9   19   29   39   49   59
[10,]   10   20   30   40   50   60
> 
> closefn.gds(f)
> 
> 
> # cteate the GDS file "test2.gds"
> (f <- createfn.gds("test2.gds"))
File: /Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck/test2.gds (70 bytes)
+    [  ]
> 
> X <- matrix(1:50, nrow=10)
> Y <- matrix((1:50)/100, nrow=10)
> Z1 <- factor(c(rep(c("ABC", "DEF", "ETD"), 3), "TTT"))
> Z2 <- c(TRUE, FALSE, TRUE, FALSE, TRUE)
> 
> node.X <- add.gdsn(f, "X", X)
> node.Y <- add.gdsn(f, "Y", Y)
> node.Z1 <- add.gdsn(f, "Z1", Z1)
> node.Z2 <- add.gdsn(f, "Z2", Z2)
> f
File: /Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck/test2.gds (379 bytes)
+    [  ]
|--+ X   { Int32 10x5, 200 bytes }
|--+ Y   { Float64 10x5, 400 bytes }
|--+ Z1   { Int32,factor 10, 40 bytes } *
|--+ Z2   { Int32,logical 5, 20 bytes } *
> 
> closefn.gds(f)
> 
> 
> 
> ###########################################################
> # apply in parallel
> 
> library(parallel)
> 
> # Use option cl.core to choose an appropriate cluster size.
> cl <- makeCluster(getOption("cl.cores", 2L))
Warning in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  :
  port 11308 cannot be opened
Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE,  : 
  cannot open the connection
Calls: makeCluster ... makePSOCKcluster -> newPSOCKnode -> socketConnection
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [318s/324s]
 [319s/324s] 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 ERROR
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

gdsfmt.Rcheck/00install.out:

* installing *source* package ‘gdsfmt’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_CoreArray.cpp -o R_CoreArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gdsfmt.cpp -o gdsfmt.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dAny.cpp -o CoreArray/dAny.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dBase.cpp -o CoreArray/dBase.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dFile.cpp -o CoreArray/dFile.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dStream.cpp -o CoreArray/dStream.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/adler32.c -o ZLIB/adler32.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/compress.c -o ZLIB/compress.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/crc32.c -o ZLIB/crc32.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/deflate.c -o ZLIB/deflate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/infback.c -o ZLIB/infback.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inffast.c -o ZLIB/inffast.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inflate.c -o ZLIB/inflate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inftrees.c -o ZLIB/inftrees.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/trees.c -o ZLIB/trees.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/uncompr.c -o ZLIB/uncompr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/zutil.c -o ZLIB/zutil.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4.c -o LZ4/lz4.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
LZ4/lz4.c:153: warning: ‘LZ4_readLE16’ defined but not used
LZ4/lz4.c:202: warning: ‘LZ4_copy4’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/xxhash.c -o LZ4/xxhash.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o gdsfmt.so R_CoreArray.o gdsfmt.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dSerial.o CoreArray/dStream.o CoreArray/dStruct.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.Rcheck/gdsfmt/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gdsfmt)

gdsfmt.Rcheck/gdsfmt-Ex.timings:

nameusersystemelapsed
add.gdsn0.1100.0120.124
addfile.gdsn0.0080.0020.010
addfolder.gdsn0.0330.0050.037
append.gdsn0.0200.0020.021
apply.gdsn0.0400.0110.051
assign.gdsn0.0270.0060.033
cache.gdsn0.0030.0010.005
cleanup.gds0.0180.0030.021
closefn.gds0.0010.0010.003