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BioC 3.2: CHECK report for ChemmineR on zin1

This page was generated on 2016-04-23 10:11:03 -0700 (Sat, 23 Apr 2016).

Package 161/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 2.22.3
Thomas Girke
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ChemmineR
Last Changed Rev: 112134 / Revision: 116712
Last Changed Date: 2016-01-04 07:35:08 -0800 (Mon, 04 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChemmineR
Version: 2.22.3
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.22.3.tar.gz
StartedAt: 2016-04-22 22:56:18 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:58:01 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 103.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ChemmineR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.22.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChemmineR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChemmineR’ version ‘2.22.3’
* 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 ‘ChemmineR’ can be installed ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ChemmineOB’
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 ... NOTE
'library' or 'require' calls in package code:
  ‘ChemmineDrugs’ ‘ChemmineOB’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘grid’
  ‘png’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘ChemmineR/R/sim.R’:
  unlockBinding(".progress_bar_int_cnt", environment(.progress_bar))

.data.frame.to.str: no visible binding for global variable ‘string’
.parseV3000: no visible binding for global variable ‘AW’
applyOptions: no visible global function definition for ‘convertFormat’
canonicalNumbering: no visible global function definition for
  ‘canonicalNumbering_OB’
canonicalNumberingOB: no visible global function definition for
  ‘canonicalNumbering_OB’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
draw_sdf: no visible global function definition for ‘fmcs’
exactMassOB: no visible global function definition for ‘exactMass_OB’
fingerprintOB: no visible global function definition for
  ‘fingerprint_OB’
getDbConn: no visible global function definition for ‘error’
handle_raster: no visible global function definition for ‘readPNG’
handle_raster: no visible global function definition for ‘rasterGrob’
handle_segs: no visible binding for global variable ‘C1’
handle_segs: no visible binding for global variable ‘C2’
handle_segs: no visible binding for global variable ‘C1.1’
handle_segs: no visible binding for global variable ‘C2.1’
handle_text: no visible binding for global variable ‘C1’
handle_text: no visible binding for global variable ‘C2’
insertDef: no visible global function definition for
  ‘dbGetPreparedQuery’
insertDescriptor: no visible global function definition for
  ‘dbGetPreparedQuery’
insertDescriptorType: no visible global function definition for
  ‘dbGetPreparedQuery’
insertFeature: no visible global function definition for
  ‘dbGetPreparedQuery’
insertNamedDef: no visible global function definition for
  ‘dbGetPreparedQuery’
parBatchByIndex: no visible global function definition for
  ‘clusterExport’
parBatchByIndex: no visible global function definition for
  ‘clusterApplyLB’
postgresqlWriteTable: no visible global function definition for
  ‘postgresqlTableRef’
postgresqlWriteTable: no visible global function definition for
  ‘postgresqlQuoteId’
postgresqlWriteTable: no visible global function definition for
  ‘postgresqlpqExec’
postgresqlWriteTable: no visible global function definition for
  ‘postgresqlCopyInDataframe’
postgresqlWriteTable: no visible global function definition for
  ‘postgresqlgetResult’
propOB: no visible global function definition for ‘prop_OB’
sdf2OBMol: no visible global function definition for ‘forEachMol’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
setPriorities: no visible global function definition for
  ‘clusterExport’
smartsSearchOB: no visible global function definition for
  ‘smartsSearch_OB’
smile2sdfFile: no visible global function definition for
  ‘convertFormatFile’
smiles2sdf: no visible global function definition for ‘convertFormat’
smiles2sdfOB: no visible global function definition for ‘convertFormat’
updatePriorities: no visible global function definition for
  ‘dbGetPreparedQuery’
* 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 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘ChemmineR/libs/ChemmineR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Objects: ‘desc.o’, ‘formats.o’, ‘script.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Object: ‘cluster.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [32s/33s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [15s/16s]
 [15s/16s] 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.


ChemmineR.Rcheck/00install.out:

* installing *source* package ‘ChemmineR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c DisjointSets.cpp -o DisjointSets.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c cluster.cc -o cluster.o
cluster.cc: In function ‘int nbr_intersect(std::vector<int>&, std::vector<int>&)’:
cluster.cc:118:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
                        ^
cluster.cc:118:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
                                             ^
cluster.cc: In function ‘int contains(int, std::vector<int>&)’:
cluster.cc:131:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < list.size(); i++)
                             ^
cluster.cc: In function ‘DisjointSets cluster(int, int, int, int)’:
cluster.cc:267:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int j = 0; j < nbr_list[i].size(); j ++) {
                                        ^
cluster.cc: In function ‘void loadNNMatrix(int, int, int, SEXP)’:
cluster.cc:284:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                      ^
cluster.cc:298:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
                    ^
cluster.cc: In function ‘void loadNNList(int, int, SEXP)’:
cluster.cc:314:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                      ^
cluster.cc:332:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(nbrs.size() < minNbrs) // will end up a singleton
                    ^
cluster.cc: In function ‘SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)’:
cluster.cc:390:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++){
                      ^
cluster.cc: At global scope:
cluster.cc:49:13: warning: ‘void prepare_neighbors(const char*, int, int)’ defined but not used [-Wunused-function]
 void static prepare_neighbors(const char* nbr_file, int skip, int p)
             ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c cstrsplit.cc -o cstrsplit.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:249:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < descs.size(); i++)
                              ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXP)’:
fingerprints.cc:138:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++)
                            ^
fingerprints.cc:145:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
                            ^
fingerprints.cc:158:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
                            ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c formats.cc -o formats.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c molecule.cc -o molecule.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function ‘SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)’:
r_wrap.cc:949:15: warning: variable ‘p’ set but not used [-Wunused-but-set-variable]
   const char *p = typeName;
               ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c script.cc -o script.o
In file included from script.cc:2:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.2-bioc/R/library/BH/include"  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c similarity.cc -o similarity.o
In file included from similarity.cc:1:0:
desc.h:39:13: warning: ‘elements’ defined but not used [-Wunused-variable]
 static char elements[112][3] = {
             ^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/ChemmineR.Rcheck/ChemmineR/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘ChemmineR’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘ChemmineR’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘ChemmineR’
Creating a generic function for ‘print’ from package ‘base’ in package ‘ChemmineR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChemmineR)

ChemmineR.Rcheck/ChemmineR-Ex.timings:

nameusersystemelapsed
AP-class0.3750.0520.427
APset-class0.3210.0280.348
ExtSDF-class0.0020.0000.001
FP-class0.0890.0000.089
FPset-class0.3580.0080.366
SDF-class0.0490.0040.053
SDF2apcmp0.020.000.02
SDFset-class0.3420.0160.359
SDFset2SDF0.1080.0040.112
SDFset2list0.0540.0080.062
SDFstr-class0.3070.0040.311
SMI-class0.0020.0000.002
SMIset-class0.0020.0010.005
addDescriptorType0.0010.0000.001
addNewFeatures2.4050.0232.430
ap0.0790.0040.083
apfp0.0030.0000.003
apset0.0040.0000.004
apset2descdb0.3250.0160.341
atomblock0.0860.0080.094
atomcount0.1730.0040.177
atomprop0.0030.0000.004
atomsubset0.0230.0010.026
batchByIndex0.0010.0000.000
bondblock0.0820.0080.090
bonds0.0260.0030.029
browseJob0.0010.0010.001
bufferLines0.0010.0000.000
bufferResultSet0.0010.0000.001
byCluster0.7910.0000.790
canonicalNumbering0.2190.0110.501
canonicalize0.0370.0000.038
cid0.0210.0000.020
cluster.sizestat0.5490.0080.557
cluster.visualize0.6690.0080.676
cmp.cluster2.1810.0162.196
cmp.duplicated0.0630.0000.063
cmp.parse0.0200.0040.022
cmp.parse1000
cmp.search0.6560.0120.667
cmp.similarity0.0160.0040.021
conMA0.0490.0080.056
connections0.1770.0040.200
datablock0.2420.0080.251
datablock2ma0.0320.0000.032
db.explain0.0440.0040.048
db.subset0.0040.0000.003
dbTransaction0.0320.0000.033
desc2fp0.0990.0080.107
draw_sdf0.3460.0000.346
exactMassOB0.6490.0000.655
findCompounds1.9520.0121.963
findCompoundsByName0.3120.0080.320
fingerprintOB0.0010.0000.000
fold0.0020.0000.001
foldCount0.0010.0000.001
fp2bit0.3890.0080.397
fpSim0.2820.0080.289
fptype0.0010.0000.001
fromNNMatrix0.820.000.82
genAPDescriptors0.0120.0040.016
genParameters0.4930.0000.492
generate3DCoords0.0000.0000.001
getAllCompoundIds0.3290.0040.333
getCompoundFeatures2.0350.0042.047
getCompoundNames0.3110.0010.311
getCompounds0.3250.0040.329
getIds000
grepSDFset0.0480.0000.047
groups0.1110.0030.116
header0.0880.0000.087
initDb0.0310.0000.032
jarvisPatrick2.0180.0042.020
jobToken-class000
launchCMTool0.0000.0000.001
listCMTools000
listFeatures0.3480.0010.349
loadSdf2.2260.0042.231
makeUnique0.0210.0000.021
maximallyDissimilar0.2410.0000.240
nearestNeighbors1.1050.0001.104
numBits0.0010.0000.001
obmol0.0310.0040.035
parBatchByIndex0.0010.0000.001
plotStruc0.3260.0000.327
propOB0.0010.0000.001
pubchemFPencoding0.0020.0000.003
read.AP0.0120.0000.016
read.SDFindex0.0150.0000.015
read.SDFset0.6080.0000.608
read.SDFstr0.8510.0000.851
read.SMIset0.0010.0000.001
regenerateCoords0.0010.0000.001
result0.0010.0000.001
rings0.4380.0000.439
sdf.subset0.0010.0000.000
sdf.visualize0.0150.0000.015
sdf2ap0.3260.0400.366
sdf2list0.0250.0040.029
sdf2smiles0.0000.0000.001
sdf2str0.0230.0040.027
sdfStream0.0160.0000.016
sdfid0.0210.0000.021
sdfsample0.0460.0000.045
sdfstr2list0.6240.1760.802
searchSim0.0010.0000.001
searchString0.0000.0000.001
selectInBatches0.0010.0000.001
setPriorities000
smartsSearchOB0.0010.0000.000
smiles2sdf0.0010.0000.001
smisample0.0030.0000.003
status0.0000.0000.001
toolDetails0.0010.0000.000
trimNeighbors1.6150.0001.616
validSDF0.0180.0040.021
view0.0560.0000.056
write.SDF0.1700.0000.171
write.SDFsplit0.0150.0000.015
write.SMI0.0020.0000.002