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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChemmineR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings ChemmineR_3.59.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/ChemmineR.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ChemmineR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ChemmineR' version '3.59.0'
* 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 whether package 'ChemmineR' can be installed ... WARNING
Found the following significant warnings:
  formats.cc:237:24: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
See 'E:/biocbuild/bbs-3.21-bioc/meat/ChemmineR.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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:
  'png'
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 code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'ChemmineDrugs' 'ChemmineOB' 'RPostgreSQL' 'RSQLite' 'fmcsR' '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'
DUD: no visible global function definition for 'download.file'
DUD: no visible global function definition for 'untar'
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'
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_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'
sdf2image: no visible global function definition for 'convertToImage'
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 browseURL canonicalNumbering_OB clusterApplyLB
  clusterExport combn convertFormat convertFormatFile convertToImage
  data dev.off download.file error exactMass_OB fingerprint_OB fmcs
  forEachMol pdf postgresqlCopyInDataframe postgresqlQuoteId
  postgresqlTableRef postgresqlgetResult postgresqlpqExec postscript
  prop_OB rainbow read.delim read.table rgb smartsSearch_OB str string
  untar write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow",
             "rgb")
  importFrom("utils", "browseURL", "combn", "data", "download.file",
             "read.delim", "read.table", "str", "untar", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) cmp.duplicated.Rd:29: Escaped LaTeX specials: \$
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'sdfid<-'
Undocumented S4 methods:
  generic '$' and siglist '_p_Descriptors'
  generic '[' and siglist 'ExternalReferenceSwig'
  generic '[<-' and siglist 'ExternalReferenceSwig'
  generic 'coerce' and siglist 'ExternalReferenceSwig,character'
  generic 'length' and siglist 'SWIGArray'
  generic 'sdfid<-' and siglist 'SDFset'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'cmp.search.Rd':
  'visualize' 'visualize.browse' 'visualize.query'
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/ChemmineR/libs/x64/ChemmineR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'ChemmineR/libs/x64/ChemmineR.dll':
  Found non-API call to R: 'SET_S4_OBJECT'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'ChemmineR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AP-class
> ### Title: Class "AP"
> ### Aliases: AP-class ap,AP-method show,AP-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("AP")
Class "AP" [package "ChemmineR"]

Slots:
              
Name:       AP
Class: numeric
> 
> ## Instance of SDFset class
> data(sdfsample)
> sdfset <- sdfsample[1:50]
> sdf <- sdfsample[[1]]
> 
> ## Compute atom pair library
> ap <- sdf2ap(sdf)
> (apset <- sdf2ap(sdfset))
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Complete output:
  > BiocGenerics:::testPackage("ChemmineR")
  ======= testing fpset ===============================================
  ======= folding... 
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 6 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/ChemmineR.Rcheck/00check.log'
for details.