| Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 64/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| HDF5Array 1.30.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
|
To the developers/maintainers of the HDF5Array package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: HDF5Array |
| Version: 1.30.1 |
| Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings HDF5Array_1.30.1.tar.gz |
| StartedAt: 2024-03-08 16:09:18 -0500 (Fri, 08 Mar 2024) |
| EndedAt: 2024-03-08 16:14:22 -0500 (Fri, 08 Mar 2024) |
| EllapsedTime: 304.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HDF5Array.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings HDF5Array_1.30.1.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-R41/meat/HDF5Array.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.30.1’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HDF5Array’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 21.2Mb
sub-directories of 1Mb or more:
extdata 7.7Mb
libs 12.5Mb
* checking package 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘rhdf5:::h5checktypeOrOpenLocS3’
See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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
File ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library/HDF5Array/libs/HDF5Array.so’:
Found ‘__printf_chk’, possibly from ‘printf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
TENxMatrix-class 92.795 25.658 65.966
h5mread 58.896 2.845 62.100
writeTENxMatrix 16.005 1.148 17.486
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/hpages/bbs-3.18-bioc-R41/meat/HDF5Array.Rcheck/00check.log’
for details.
HDF5Array.Rcheck/00install.out
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### Running command:
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### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL HDF5Array
###
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* installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5File.c -o H5File.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5DSetDescriptor.c -o H5DSetDescriptor.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5dimscales.c -o h5dimscales.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c uaselection.c -o uaselection.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5mread_helpers.c -o h5mread_helpers.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c ChunkIterator.c -o ChunkIterator.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5mread_index.c -o h5mread_index.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: ‘NOT_USED_make_nzindex_from_bufs’ defined but not used [-Wunused-function]
206 | static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: ‘NOT_USED_make_nzdata_from_IntAE_bufs’ defined but not used [-Wunused-function]
179 | static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: ‘NOT_USED_make_nzindex_from_buf’ defined but not used [-Wunused-function]
123 | static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5mread.c -o h5mread.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5summarize.c -o h5summarize.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -shared -L/home/hpages/bbs-3.18-bioc-R41/R/lib -L/usr/local/lib -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/hpages/bbs-3.18-bioc-R41/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/hpages/bbs-3.18-bioc-R41/R/lib -lR
installing to /home/hpages/bbs-3.18-bioc-R41/R/site-library/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (HDF5Array)
HDF5Array.Rcheck/tests/run_unitTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, 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.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
Loading required package: rhdf5
Attaching package: 'HDF5Array'
The following object is masked from 'package:rhdf5':
h5ls
[1] TRUE
> HDF5Array:::.test()
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:SparseArray':
rowMedians
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/hpages/.cache/R/basilisk/1.14.3/zellkonverter/1.12.1/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
RUNIT TEST PROTOCOL -- Fri Mar 8 16:14:19 2024
***********************************************
Number of test functions: 15
Number of errors: 0
Number of failures: 0
1 Test Suite :
HDF5Array RUnit Tests - 15 test functions, 0 errors, 0 failures
Number of test functions: 15
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
30.914 2.017 32.628
HDF5Array.Rcheck/HDF5Array-Ex.timings
| name | user | system | elapsed | |
| H5ADMatrix-class | 2.824 | 0.124 | 2.949 | |
| H5ADMatrixSeed-class | 0.072 | 0.016 | 0.088 | |
| H5File-class | 0.368 | 0.020 | 3.293 | |
| H5SparseMatrix-class | 0.090 | 0.000 | 0.092 | |
| H5SparseMatrixSeed-class | 0.001 | 0.000 | 0.001 | |
| HDF5Array-class | 1.961 | 0.288 | 3.199 | |
| HDF5ArraySeed-class | 0.087 | 0.000 | 0.088 | |
| ReshapedHDF5Array-class | 0.103 | 0.000 | 0.103 | |
| ReshapedHDF5ArraySeed-class | 0.054 | 0.000 | 0.054 | |
| TENxMatrix-class | 92.795 | 25.658 | 65.966 | |
| TENxMatrixSeed-class | 2.361 | 0.273 | 2.922 | |
| dump-management | 0.324 | 0.068 | 0.392 | |
| h5ls | 0.006 | 0.003 | 0.009 | |
| h5mread | 58.896 | 2.845 | 62.100 | |
| h5mread_from_reshaped | 0.223 | 0.008 | 0.231 | |
| h5writeDimnames | 0.622 | 0.016 | 0.639 | |
| saveHDF5SummarizedExperiment | 0.642 | 0.024 | 0.665 | |
| writeHDF5Array | 0.418 | 0.012 | 0.431 | |
| writeTENxMatrix | 16.005 | 1.148 | 17.486 | |