Samuela Pollack
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/rhdf5client |
| Branch: master |
| Last Commit: 3d1161e |
| Last Changed Date: 2018-12-03 16:11:13 -0400 (Mon, 03 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:49:24 -0400 (Tue, 09 Apr 2019).
| Package 1345/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rhdf5client 1.5.1 Samuela Pollack
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: rhdf5client |
| Version: 1.5.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rhdf5client.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rhdf5client_1.5.1.tar.gz |
| StartedAt: 2019-04-09 03:13:10 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:15:42 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 152.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rhdf5client.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rhdf5client.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rhdf5client_1.5.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rhdf5client.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.5.1’
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘getDataList’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HSDS_Matrix: warning in readBin(GET(targ)$content, w = "character"):
partial argument match of 'w' to 'what'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'H5S_dataset,character,character,ANY'
generic '[' and siglist 'H5S_dataset,numeric,numeric,ANY'
generic '[' and siglist 'HSDSDataset,numeric,numeric,ANY'
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 ... WARNING
Duplicated \argument entries in documentation object 'dim':
‘x’
Duplicated \argument entries in documentation object 'dimnames,H5S_ArraySeed-method':
‘x’
Duplicated \argument entries in documentation object '[,H5S_dataset,numeric,numeric-method':
‘x’ ‘i’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 0.088 0 10.494
* 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: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/rhdf5client.Rcheck/00check.log’
for details.
rhdf5client.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rhdf5client
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘rhdf5client’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o rhdf5client.so extract.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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, colMeans, colSums, 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, rowMeans, rowSums,
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 FAILED: 0
>
> proc.time()
user system elapsed
16.359 3.840 26.749
rhdf5client.Rcheck/rhdf5client-Ex.timings
| name | user | system | elapsed | |
| H5S_Array | 0 | 0 | 0 | |
| H5S_dataset2 | 0.379 | 0.004 | 1.094 | |
| H5S_source-class | 0.096 | 0.001 | 0.711 | |
| HSDSDataset | 0.064 | 0.003 | 0.963 | |
| HSDSFile | 0.015 | 0.004 | 0.263 | |
| HSDSSource | 0.001 | 0.000 | 0.001 | |
| HSDS_Matrix | 0.214 | 0.008 | 1.087 | |
| HSDS_Matrix_OLD | 0.000 | 0.000 | 0.001 | |
| URL_h5serv | 0.000 | 0.000 | 0.001 | |
| URL_hsds | 0.000 | 0.000 | 0.001 | |
| domains | 0.035 | 0.000 | 0.553 | |
| dsmeta | 0 | 0 | 0 | |
| fetchDatasets | 0.041 | 0.001 | 0.437 | |
| getData-methods | 0.103 | 0.008 | 1.396 | |
| getDatasetAttrs | 0.041 | 0.004 | 0.478 | |
| getDatasetSlice | 0.031 | 0.000 | 0.366 | |
| getDatasetUUIDs | 0.022 | 0.000 | 0.272 | |
| getDims | 0.023 | 0.001 | 0.277 | |
| getHRDF | 0.059 | 0.004 | 0.509 | |
| groups-methods | 0.000 | 0.000 | 0.001 | |
| hsdsInfo | 0.030 | 0.000 | 0.293 | |
| internalDim | 0 | 0 | 0 | |
| links | 0 | 0 | 0 | |
| listDatasets | 0.052 | 0.008 | 0.872 | |
| listDomains-methods | 0.088 | 0.000 | 10.494 | |
| setPath | 0.015 | 0.000 | 0.184 | |
| sproc | 0.003 | 0.000 | 0.003 | |
| targets | 0.001 | 0.000 | 0.000 | |