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BioC 3.5: CHECK report for ChemmineR on malbec2

This page was generated on 2017-08-16 13:13:14 -0400 (Wed, 16 Aug 2017).

Package 201/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 2.28.1
Thomas Girke
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChemmineR
Last Changed Rev: 130824 / Revision: 131943
Last Changed Date: 2017-06-30 17:37:15 -0400 (Fri, 30 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ChemmineR
Version: 2.28.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.28.1.tar.gz
StartedAt: 2017-08-15 21:49:08 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:51:01 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 113.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ChemmineR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ChemmineR_2.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ChemmineR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.28.1’
* 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 ‘ChemmineR’ can be installed ... 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 global function definition for
  ‘write.table’
.data.frame.to.str: no visible binding for global variable ‘string’
.parseV3000: no visible binding for global variable ‘AW’
.rings: no visible global function definition for ‘combn’
applyOptions: no visible global function definition for ‘convertFormat’
browseJob: no visible global function definition for ‘browseURL’
canonicalNumbering: no visible global function definition for
  ‘canonicalNumbering_OB’
canonicalNumberingOB: no visible global function definition for
  ‘canonicalNumbering_OB’
cluster.visualize: no visible global function definition for ‘rainbow’
cluster.visualize: no visible global function definition for ‘pdf’
cluster.visualize: no visible global function definition for
  ‘postscript’
cluster.visualize: no visible global function definition for ‘dev.off’
concatenate_plots: no visible binding for global variable ‘arrangeGrob’
desc2fp: no visible global function definition for ‘data’
draw_sdf: no visible global function definition for ‘rgb’
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’
getCompoundFeatures : <anonymous>: no visible global function
  definition for ‘write.table’
getCompounds: no visible global function definition for ‘str’
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’
listCMTools: no visible global function definition for ‘read.table’
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’
read.AP: no visible global function definition for ‘read.delim’
sdf2OBMol: no visible global function definition for ‘forEachMol’
sdf2smiles: no visible global function definition for ‘convertFormat’
sdf2smilesOB: no visible global function definition for ‘convertFormat’
sdfStream: no visible global function definition for ‘write.table’
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’
write.SMI: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  AW C1 C1.1 C2 C2.1 arrangeGrob browseURL canonicalNumbering_OB
  clusterApplyLB clusterExport combn convertFormat convertFormatFile
  data dev.off error exactMass_OB fingerprint_OB fmcs forEachMol pdf
  postgresqlCopyInDataframe postgresqlQuoteId postgresqlTableRef
  postgresqlgetResult postgresqlpqExec postscript prop_OB rainbow
  rasterGrob read.delim read.table readPNG rgb smartsSearch_OB str
  string write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
             "rgb")
  importFrom("utils", "browseURL", "combn", "data", "read.delim",
             "read.table", "str", "write.table")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.5-bioc/meat/ChemmineR.Rcheck/00check.log’
for details.


ChemmineR.Rcheck/00install.out:

* installing *source* package ‘ChemmineR’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c DisjointSets.cpp -o DisjointSets.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/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:118:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while (i < nbrs1.size() and j < nbrs2.size()) {
           ^
cluster.cc:118:32: 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:131:17: 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:267:21: 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:284:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                     ^
cluster.cc:298:18: 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:314:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned i=0; i<N; i++) //rows
                     ^
cluster.cc:332:18: 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:390:21: 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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c cstrsplit.cc -o cstrsplit.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c desc.cc -o desc.o
desc.cc: In function ‘SEXPREC* genAPDescriptor(SEXP)’:
desc.cc:249:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < descs.size(); i++)
                 ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function ‘SEXPREC* uniquifyAtomPairs(SEXP)’:
fingerprints.cc:138:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++)
                 ^
fingerprints.cc:145:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
                 ^
fingerprints.cc:158:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0; i < aps.size(); i++){
                 ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c formats.cc -o formats.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fpic  -g -O2  -Wall -c molecule.cc -o molecule.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/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-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/BH/include" -I/usr/local/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-3.5-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-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/ChemmineR.Rcheck/ChemmineR/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 (ChemmineR)

ChemmineR.Rcheck/ChemmineR-Ex.timings:

nameusersystemelapsed
AP-class0.5120.0400.550
APset-class0.5680.0440.612
ExtSDF-class0.0000.0000.001
FP-class0.0800.0000.084
FPset-class0.4160.0040.422
SDF-class0.0440.0000.045
SDF2apcmp0.020.000.02
SDFset-class0.3360.0160.353
SDFset2SDF0.0840.0000.083
SDFset2list0.0280.0200.049
SDFstr-class0.2480.0000.247
SMI-class0.0040.0000.002
SMIset-class0.0040.0000.005
addDescriptorType000
addNewFeatures3.2480.0403.306
ap0.0640.0080.070
apfp0.0040.0000.002
apset0.0040.0000.004
apset2descdb0.2600.0160.274
atomblock0.0840.0040.090
atomcount0.1520.0040.157
atomprop0.0040.0000.003
atomsubset0.1040.0000.104
batchByIndex0.0000.0000.001
bondblock0.0640.0040.068
bonds0.0280.0000.028
browseJob000
bufferLines000
bufferResultSet0.0000.0000.001
byCluster0.680.000.68
canonicalNumbering0.2200.0040.261
canonicalize0.0960.0000.095
cid0.020.000.02
cluster.sizestat0.4960.0080.506
cluster.visualize0.4960.0000.498
cmp.cluster1.6520.0041.655
cmp.duplicated0.060.000.06
cmp.parse0.0240.0000.024
cmp.parse1000
cmp.search0.5520.0000.549
cmp.similarity0.020.000.02
conMA0.0480.0000.048
connections0.4160.0080.465
datablock0.2360.0040.238
datablock2ma0.0520.0000.053
db.explain0.0320.0000.033
db.subset0.0040.0000.003
dbTransaction0.0200.0000.019
desc2fp0.1120.0000.115
draw_sdf1.3280.0041.337
exactMassOB0.5480.0000.567
findCompounds2.3280.0082.339
findCompoundsByName0.2560.0000.259
fingerprintOB000
fold0.0000.0000.001
foldCount0.0120.0000.015
fp2bit0.2360.0040.236
fpSim0.360.000.36
fptype0.0000.0000.001
fromNNMatrix0.6720.0000.672
genAPDescriptors0.0080.0040.015
genParameters0.4200.0000.422
generate3DCoords000
getAllCompoundIds0.3320.0000.336
getCompoundFeatures1.9640.0081.977
getCompoundNames0.2640.0000.265
getCompounds0.4360.0000.436
getIds0.0040.0000.001
grepSDFset0.0840.0000.087
groups0.1720.0040.176
header0.0640.0000.065
initDb0.0160.0000.017
jarvisPatrick1.5120.0001.515
jobToken-class000
launchCMTool0.0000.0000.001
listCMTools000
listFeatures0.2680.0040.272
loadSdf2.1120.0002.115
makeUnique0.0160.0000.016
maximallyDissimilar0.1880.0000.187
nearestNeighbors0.90.00.9
numBits0.0000.0000.001
obmol0.0280.0000.027
parBatchByIndex000
plotStruc0.1920.0040.197
propOB000
pubchemFPencoding0.0040.0000.002
read.AP0.0160.0000.017
read.SDFindex0.020.000.02
read.SDFset0.5560.0000.556
read.SDFstr1.0120.0001.015
read.SMIset0.0040.0000.002
regenerateCoords000
result000
rings0.4720.0040.472
sdf.subset000
sdf.visualize0.0160.0000.014
sdf2ap0.2520.0160.267
sdf2list0.0160.0040.022
sdf2smiles000
sdf2str0.0240.0000.025
sdfStream0.0160.0000.015
sdfid0.0160.0000.016
sdfsample0.0360.0000.039
sdfstr2list0.5400.1160.657
searchSim000
searchString0.0000.0000.001
selectInBatches0.0000.0000.001
setPriorities000
smartsSearchOB000
smiles2sdf000
smisample0.0040.0000.002
status0.0000.0000.001
toolDetails0.0000.0000.001
trimNeighbors1.0520.0001.052
validSDF0.0200.0000.018
view0.0360.0040.041
write.SDF0.1240.0000.124
write.SDFsplit0.0160.0000.015
write.SMI0.0000.0000.002