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CHECK report for fmcsR on merida1

This page was generated on 2021-05-06 12:35:01 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the fmcsR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 642/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fmcsR 1.32.0  (landing page)
Thomas Girke
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/fmcsR
Branch: RELEASE_3_12
Last Commit: 91d402d
Last Changed Date: 2020-10-27 10:46:59 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: fmcsR
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fmcsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fmcsR_1.32.0.tar.gz
StartedAt: 2021-05-06 01:52:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:53:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 84.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: fmcsR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:fmcsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings fmcsR_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/fmcsR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fmcsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fmcsR’ version ‘1.32.0’
* 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 ‘fmcsR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘ChemmineR’
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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Failed with error:  ‘there is no package called ‘bibtex’’
  Error in (function (bibtype, textVersion = NULL, header = NULL, footer = NULL,     key = NULL, ..., other = list(), mheader = NULL, mfooter = NULL) {    BibTeX_names <- names(BibLaTeX_entry_field_db)    args <- c(list(...), other)    if (!length(args))         return(structure(list(), class = "bibentry"))    if (any(vapply(names(args), .is_not_nonempty_text, FALSE)))         stop("all fields have to be named")    args <- c(list(bibtype = bibtype, textVersion = textVersion,         header = header, footer = footer, key = key), list(...))    args <- lapply(args, .listify)    other <- lapply(other, .listify)    max_length <- max(vapply(c(args, other), length, 0L))    args_length <- vapply(args, length, 0L)    if (!all(args_length_ok <- args_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, %s: %s",             "the following need to be recycled", paste(names(args)[!args_length_ok],                 collapse = ", ")), domain = NA)    args <- lapply(args, function(x) rep(x, length.out = max_length))    other_length <- vapply(other, length, 0L)    if (!all(other_length_ok <- other_length %in% c(1L, max_length)))         warning(gettextf("Not all arguments are of the same length, %s: %s",             "the following need to be recycled", paste(names(other)[!other_length_ok],                 collapse = ", ")), domain = NA)    other <- lapply(other, function(x) rep(x, length.out = max_length))    bibentry1 <- function(bibtype, textVersion, header = NULL,         footer = NULL, key = NULL, ..., other = list()) {        bibtype <- as.character(bibtype)        stopifnot(length(bibtype) == 1L)        pos <- match(tolower(bibtype), tolower(BibTeX_names))        if (is.na(pos))             stop(gettextf("%s has to be one of %s", sQuote("bibtype"),                 paste(BibTeX_names, collapse = ", ")), domain = NA)        bibtype <- BibTeX_names[pos]        rval <- c(list(...), other)        rval <- rval[!vapply(rval, .is_not_nonempty_text, FALSE)]        fields <- tolower(names(rval))        names(rval) <- fields        attr(rval, "bibtype") <- bibtype        .BibEntryCheckBibEntry1(rval)        pos <- fields %in% .BibEntryNameList        if (any(pos)) {            for (i in which(pos)) if (!inherits(rval[[i]], "person"))                 rval[[i]] <- ArrangeAuthors(rval[[i]])        }        pos <- fields %in% c("dateobj") | pos        if (any(!pos)) {            for (i in which(!pos)) rval[[i]] <- as.character(rval[[i]])        }        attr(rval, "key") <- if (is.null(key))             NULL        else as.character(key)        if (is.null(rval[["dateobj"]])) {            tdate <- try(ProcessDates(rval), TRUE)            if (!inherits(tdate, "try-error"))                 attr(rval, "dateobj") <- tdate        }        else {            attr(rval, "dateobj") <- rval[["dateobj"]]            rval[["dateobj"]] <- NULL        }        if (!is.null(textVersion))             attr(rval, "textVersion") <- as.character(textVersion)        if (!.is_not_nonempty_text(header))             attr(rval, "header") <- paste(header, collapse = "\n")        if (!.is_not_nonempty_text(footer))             attr(rval, "footer") <- paste(footer, collapse = "\n")        return(rval)    }    rval <- lapply(seq_along(args$bibtype), function(i) do.call("bibentry1",         c(lapply(args, "[[", i), list(other = lapply(other, "[[",             i)))))    if (!.is_not_nonempty_text(mheader))         attr(rval, "mheader") <- paste(mheader, collapse = "\n")    if (!.is_not_nonempty_text(mfooter))         attr(rval, "mfooter") <- paste(mfooter, collapse = "\n")    class(rval) <- c("BibEntry", "bibentry")    rval})(year = "2021", key = "_2021"): argument "bibtype" is missing, with no default
* 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' call to ‘ChemmineR’ which was already attached by Depends.
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘RUnit’ ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fmcs: no visible global function definition for ‘as’
fmcs: no visible global function definition for ‘new’
fmcsBatch: no visible global function definition for ‘as’
fmcsBatch : score: no visible global function definition for ‘as’
plotMCS: no visible global function definition for ‘par’
coerce,list-MCS: no visible global function definition for ‘new’
Undefined global functions or variables:
  as new par
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "as", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
fmcsR-package 1.903  0.049  11.740
fmcsBatch     0.177  0.021  10.383
* 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 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/fmcsR.Rcheck/00check.log’
for details.



Installation output

fmcsR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL fmcsR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘fmcsR’ ...
** using staged installation
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
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 for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MCS.cpp -o MCS.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MCSCompound.cpp -o MCSCompound.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MCSMap.cpp -o MCSMap.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c MCSRingDetector.cpp -o MCSRingDetector.o
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
        int aromaticCount = 0;
            ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
fmcs_R_wrap.cpp:47:13: warning: variable 'matchType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default: 
            ^~~~~~~
fmcs_R_wrap.cpp:74:13: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
            ^~~~~~~~~
fmcs_R_wrap.cpp:42:6: note: variable 'matchType' is declared here
        MCS::MatchType matchType;
        ^
fmcs_R_wrap.cpp:56:13: warning: variable 'runningMode' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default:
            ^~~~~~~
fmcs_R_wrap.cpp:74:24: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
                       ^~~~~~~~~~~
fmcs_R_wrap.cpp:52:9: note: variable 'runningMode' is declared here
        MCS::RunningMode runningMode;
        ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c util.cpp -o util.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-fmcsR/00new/fmcsR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fmcsR)

Tests output


Example timings

fmcsR.Rcheck/fmcsR-Ex.timings

nameusersystemelapsed
MCS-class1.5350.0351.574
fmcs1.9390.0341.975
fmcsBatch 0.177 0.02110.383
fmcsR-package 1.903 0.04911.740
fmcstest0.0290.0070.036
mcs2sdfset0.5620.0210.584
plotMCS0.5430.0140.558