Patryk Orzechowski
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/runibic |
| Branch: RELEASE_3_9 |
| Last Commit: a3c898e |
| Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:01:22 -0400 (Wed, 16 Oct 2019).
| Package 1439/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| runibic 1.6.0 Patryk Orzechowski
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: runibic |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:runibic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings runibic_1.6.0.tar.gz |
| StartedAt: 2019-10-16 06:30:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:34:07 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 235.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: runibic.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:runibic.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings runibic_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/runibic.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘runibic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘runibic’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘runibic’ can be installed ... WARNING
Found the following significant warnings:
GlobalDefs.cpp:280:37: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/runibic.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runibic 23.623 7.469 5.969
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/runibic.Rcheck/00check.log’
for details.
runibic.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL runibic
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘runibic’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c GlobalDefs.cpp -o GlobalDefs.o
GlobalDefs.cpp:117:7: warning: unused variable 'colNum' [-Wunused-variable]
int colNum = gParameters.ColNumber;
^
GlobalDefs.cpp:280:37: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
for (auto i=maxRecord.size()-1;i>=0;i--) {
~^ ~
GlobalDefs.cpp:232:16: warning: unused variable 'rank' [-Wunused-variable]
int maxvalue,rank;
^
In file included from GlobalDefs.cpp:34:
./fibpriv.h:54:13: warning: unused function 'fh_initheap' [-Wunused-function]
static void fh_initheap(struct fibheap *);
^
./fibpriv.h:55:13: warning: unused function 'fh_insertrootlist' [-Wunused-function]
static void fh_insertrootlist(struct fibheap *, struct fibheap_el *);
^
./fibpriv.h:56:13: warning: unused function 'fh_removerootlist' [-Wunused-function]
static void fh_removerootlist(struct fibheap *, struct fibheap_el *);
^
./fibpriv.h:57:13: warning: unused function 'fh_consolidate' [-Wunused-function]
static void fh_consolidate(struct fibheap *);
^
./fibpriv.h:58:13: warning: unused function 'fh_heaplink' [-Wunused-function]
static void fh_heaplink(struct fibheap *h, struct fibheap_el *y,
^
./fibpriv.h:60:13: warning: unused function 'fh_cut' [-Wunused-function]
static void fh_cut(struct fibheap *, struct fibheap_el *, struct fibheap_el *);
^
./fibpriv.h:61:13: warning: unused function 'fh_cascading_cut' [-Wunused-function]
static void fh_cascading_cut(struct fibheap *, struct fibheap_el *);
^
./fibpriv.h:62:27: warning: unused function 'fh_extractminel' [-Wunused-function]
static struct fibheap_el *fh_extractminel(struct fibheap *);
^
./fibpriv.h:63:13: warning: unused function 'fh_checkcons' [-Wunused-function]
static void fh_checkcons(struct fibheap *h);
^
./fibpriv.h:64:13: warning: unused function 'fh_destroyheap' [-Wunused-function]
static void fh_destroyheap(struct fibheap *h);
^
./fibpriv.h:65:12: warning: unused function 'fh_compare' [-Wunused-function]
static int fh_compare(struct fibheap *h, struct fibheap_el *a,
^
./fibpriv.h:67:12: warning: unused function 'fh_comparedata' [-Wunused-function]
static int fh_comparedata(struct fibheap *h, int key, void *data,
^
./fibpriv.h:69:13: warning: unused function 'fh_insertel' [-Wunused-function]
static void fh_insertel(struct fibheap *h, struct fibheap_el *x);
^
./fibpriv.h:70:13: warning: unused function 'fh_deleteel' [-Wunused-function]
static void fh_deleteel(struct fibheap *h, struct fibheap_el *x);
^
./fibpriv.h:86:27: warning: unused function 'fhe_newelem' [-Wunused-function]
static struct fibheap_el *fhe_newelem(void);
^
./fibpriv.h:87:13: warning: unused function 'fhe_initelem' [-Wunused-function]
static void fhe_initelem(struct fibheap_el *);
^
./fibpriv.h:88:13: warning: unused function 'fhe_insertafter' [-Wunused-function]
static void fhe_insertafter(struct fibheap_el *a, struct fibheap_el *b);
^
./fibpriv.h:90:27: warning: unused function 'fhe_remove' [-Wunused-function]
static struct fibheap_el *fhe_remove(struct fibheap_el *a);
^
21 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c fib.c -o fib.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c runibic.cpp -o runibic.o
runibic.cpp:567:13: warning: unused variable 'temp' [-Wunused-variable]
int temp;
^
1 warning generated.
clang++ -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 runibic.so GlobalDefs.o RcppExports.o fib.o runibic.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-runibic/00new/runibic/libs
** R
** 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 (runibic)
runibic.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(runibic)
Loading required package: biclust
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
Loading required package: lattice
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("runibic")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
11.340 1.733 11.642
runibic.Rcheck/runibic-Ex.timings
| name | user | system | elapsed | |
| backtrackLCS | 0.001 | 0.001 | 0.012 | |
| calculateLCS | 0.004 | 0.003 | 0.003 | |
| cluster | 0.009 | 0.007 | 0.004 | |
| pairwiseLCS | 0.003 | 0.003 | 0.001 | |
| runiDiscretize | 0.015 | 0.011 | 0.008 | |
| runibic | 23.623 | 7.469 | 5.969 | |
| set_runibic_params | 0.001 | 0.001 | 0.001 | |
| unisort | 0.002 | 0.002 | 0.001 | |