Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R [S] T  U  V  W  X  Y  Z 

Package 609/671HostnameOS / ArchBUILDCHECKBUILD BIN
spade 1.8.0
Michael Linderman
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/spade
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 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: spade
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spade_1.8.0.tar.gz
StartedAt: 2013-05-01 11:09:57 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:12:22 -0700 (Wed, 01 May 2013)
EllapsedTime: 144.3 seconds
RetCode: 0
Status:  OK 
CheckDir: spade.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/spade.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 'spade/DESCRIPTION' ... OK
* this is package 'spade' version '1.8.0'
* 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 'spade' can be installed ... [16s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 compilation flags in Makevars ... 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 ... [46s/46s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
SPADE.driver 40.797  0.486   41.98
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/spade.Rcheck/00check.log'
for details.

spade.Rcheck/00install.out:

* installing *source* package 'spade' ...
checking for gcc... clang
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking how to run the C++ preprocessor... clang++ -E
checking for clang option to support OpenMP... unsupported
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking parallel/algorithm usability... no
checking parallel/algorithm presence... no
checking for parallel/algorithm... no
"Parallel STL not found using default"
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cluster.cc -o cluster.o
cluster.cc:225:29: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        size_t num_valid = c_end - c_beg;
                               ˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜^˜˜˜˜˜˜
cluster.cc:277:15: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
                                assgn[(*b - data) / dim] = cur_Id;
                                       ˜˜˜^˜˜˜˜˜  ˜
cluster.cc:301:39: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
                PROTECT(assgn = allocVector(INTSXP, obs)); n_protected++;
                                ˜˜˜˜˜˜˜˜˜˜˜         ^˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c downsample.cc -o downsample.o
downsample.cc:119:42: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        PROTECT(densities = allocVector(INTSXP, obs));
                            ˜˜˜˜˜˜˜˜˜˜˜         ^˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c spade.cc -o spade.o
spade.cc:8:31: warning: unused variable '_CallFun' [-Wunused-variable]
        static const R_CallMethodDef _CallFun[] = {
                                     ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DPACKAGE_NAME=\"spade\" -DPACKAGE_TARNAME=\"spade\" -DPACKAGE_VERSION=\"0.20\" -DPACKAGE_STRING=\"spade\ 0.20\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c upsample.cc -o upsample.o
upsample.cc:43:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'Idx_t' (aka 'int') [-Wshorten-64-to-32]
                    min_idx = j; 
                            ˜ ^
upsample.cc:67:39: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'R_xlen_t' (aka 'long') [-Wsign-conversion]
        PROTECT(assign = allocVector(INTSXP, obs)); ++n_protected;
                         ˜˜˜˜˜˜˜˜˜˜˜         ^˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
2 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o spade.so cluster.o downsample.o spade.o upsample.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/spade.Rcheck/spade/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 (spade)

spade.Rcheck/spade-Ex.timings:

nameusersystemelapsed
SPADE.FCSToTree0.0170.0020.019
SPADE.addClusterToFCS0.0230.0020.025
SPADE.addDensityToFCS0.0130.0010.014
SPADE.annotateGraph0.0130.0000.014
SPADE.downsampleFCS0.0140.0000.014
SPADE.driver40.797 0.48641.980
SPADE.flattenAnnotations0.0090.0070.015
SPADE.installPlugin0.0070.0030.009
SPADE.layout.arch0.0090.0050.014
SPADE.markerMedians0.0090.0070.016
SPADE.plot.trees0.0140.0070.021
SPADE.read.FCS0.0800.0170.097
SPADE.write.graph0.0080.0040.012