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 12:34:50 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5client.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rhdf5client_1.5.1.tar.gz |
| StartedAt: 2019-04-09 05:23:11 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:32:00 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 529.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rhdf5client.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rhdf5client.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings rhdf5client_1.5.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/rhdf5client.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/rhdf5client/libs/i386/rhdf5client.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/rhdf5client/libs/x64/rhdf5client.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
listDomains-methods 0.05 0.03 10.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
listDomains-methods 0.01 0 10.45
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/rhdf5client.Rcheck/00check.log'
for details.
rhdf5client.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rhdf5client_1.5.1.tar.gz && rm -rf rhdf5client.buildbin-libdir && mkdir rhdf5client.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rhdf5client.buildbin-libdir rhdf5client_1.5.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rhdf5client_1.5.1.zip && rm rhdf5client_1.5.1.tar.gz rhdf5client_1.5.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 302k 100 302k 0 0 4892k 0 --:--:-- --:--:-- --:--:-- 5499k
install for i386
* installing *source* package 'rhdf5client' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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]);
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o rhdf5client.dll tmp.def extract.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/rhdf5client.buildbin-libdir/00LOCK-rhdf5client/00new/rhdf5client/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'rhdf5client'
finding HTML links ... done
H5S_Array-class html
H5S_Array html
H5S_ArraySeed-class html
H5S_Matrix-class html
H5S_dataset html
H5S_dataset2 html
H5S_source-class html
HSDSArray html
HSDSArraySeed html
HSDSDataset-class html
HSDSDataset html
HSDSFile-class html
HSDSFile html
HSDSMatrix html
HSDSSource-class html
HSDSSource html
HSDS_Matrix html
HSDS_Matrix_OLD html
URL_h5serv html
URL_hsds html
as html
dataset html
dim html
dimnames html
domains html
dsmeta html
extract-methods html
extract_array html
fetchDatasets html
getData-methods html
getDatasetAttrs html
getDatasetSlice html
getDatasetUUIDs html
getDims html
getHRDF html
getReq html
groups-methods html
hsdsInfo html
internalDim html
links html
listDatasets html
listDomains-methods html
rhdf5client html
setPath html
sproc html
targets html
transfermode html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'rhdf5client' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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]);
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rhdf5client.dll tmp.def extract.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/rhdf5client.buildbin-libdir/rhdf5client/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5client' as rhdf5client_1.5.1.zip
* DONE (rhdf5client)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rhdf5client' successfully unpacked and MD5 sums checked
|
rhdf5client.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
12.67 3.42 22.81
|
rhdf5client.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
16.48 3.45 27.06
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rhdf5client.Rcheck/examples_i386/rhdf5client-Ex.timings
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rhdf5client.Rcheck/examples_x64/rhdf5client-Ex.timings
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