Vincent Carey
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/rhdf5client |
| Branch: RELEASE_3_10 |
| Last Commit: 875b34e |
| Last Changed Date: 2019-10-29 13:10:52 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:13:23 -0400 (Wed, 15 Apr 2020).
| Package 1429/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rhdf5client 1.8.0 Vincent Carey
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: rhdf5client |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:rhdf5client.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rhdf5client_1.8.0.tar.gz |
| StartedAt: 2020-04-15 05:14:28 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:17:07 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 159.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rhdf5client.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:rhdf5client.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings rhdf5client_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/rhdf5client.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhdf5client/DESCRIPTION’ ... OK
* this is package ‘rhdf5client’ version ‘1.8.0’
* 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 ‘rhdf5client’ can be installed ... OK
* 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 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
listDomains-methods 0.064 0 10.435
* 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 NOTE
See
‘/home/biocbuild/bbs-3.10-bioc/meat/rhdf5client.Rcheck/00check.log’
for details.
rhdf5client.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL rhdf5client
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘rhdf5client’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c extract.c -o extract.o
extract.c: In function ‘extractBin’:
extract.c:101:42: warning: ‘rdp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
^
extract.c:101:52: warning: ‘rip’ may be used uninitialized in this function [-Wmaybe-uninitialized]
A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
^
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o rhdf5client.so extract.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-rhdf5client/00new/rhdf5client/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 (rhdf5client)
rhdf5client.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(rhdf5client)
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
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: 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("rhdf5client")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 19 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
20.296 3.468 29.881
rhdf5client.Rcheck/rhdf5client-Ex.timings
| name | user | system | elapsed | |
| H5S_Array | 0.000 | 0.000 | 0.001 | |
| H5S_dataset2 | 0 | 0 | 0 | |
| H5S_source-class | 0 | 0 | 0 | |
| HSDSArray | 0.168 | 0.000 | 0.928 | |
| HSDSDataset | 0.064 | 0.000 | 0.983 | |
| HSDSFile | 0.012 | 0.004 | 0.268 | |
| HSDSSource | 0.000 | 0.000 | 0.001 | |
| HSDS_Matrix | 0 | 0 | 0 | |
| HSDS_Matrix_OLD | 0 | 0 | 0 | |
| URL_h5serv | 0 | 0 | 0 | |
| URL_hsds | 0 | 0 | 0 | |
| domains | 0 | 0 | 0 | |
| dsmeta | 0 | 0 | 0 | |
| fetchDatasets | 0 | 0 | 0 | |
| getData-methods | 0.184 | 0.004 | 1.493 | |
| getDatasetAttrs | 0.000 | 0.000 | 0.001 | |
| getDatasetSlice | 0 | 0 | 0 | |
| getDatasetUUIDs | 0 | 0 | 0 | |
| getDims | 0 | 0 | 0 | |
| getHRDF | 0 | 0 | 0 | |
| groups-methods | 0 | 0 | 0 | |
| hsdsInfo | 0 | 0 | 0 | |
| internalDim | 0 | 0 | 0 | |
| links | 0 | 0 | 0 | |
| listDatasets | 0.060 | 0.000 | 0.903 | |
| listDomains-methods | 0.064 | 0.000 | 10.435 | |
| setPath | 0 | 0 | 0 | |
| sproc | 0.004 | 0.000 | 0.004 | |
| targets | 0 | 0 | 0 | |