Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:50 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the rhdf5 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1573/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rhdf5 2.36.0 (landing page) Mike Smith
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: rhdf5 |
Version: 2.36.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rhdf5_2.36.0.tar.gz |
StartedAt: 2021-10-14 11:19:29 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:20:01 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 32.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rhdf5.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rhdf5_2.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/rhdf5.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rhdf5/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rhdf5’ version ‘2.36.0’ * 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 ‘rhdf5’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.7Mb sub-directories of 1Mb or more: libs 9.1Mb * 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 shell scripts ... 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/biocbuild/bbs-3.13-bioc/R/library/rhdf5/libs/rhdf5.so’: Found ‘abort’, possibly from ‘abort’ (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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/rhdf5.Rcheck/00check.log’ for details.
rhdf5.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5A.c -o H5A.o H5A.c: In function ‘H5Aread_helper_INTEGER’: H5A.c:142:10: warning: unused variable ‘herr’ [-Wunused-variable] 142 | herr_t herr = H5Aread(attr_id, mem_type_id, buf ); | ^~~~ H5A.c: In function ‘H5Aread_helper_FLOAT’: H5A.c:175:10: warning: unused variable ‘herr’ [-Wunused-variable] 175 | herr_t herr = H5Aread(attr_id, mem_type_id, buf ); | ^~~~ H5A.c: In function ‘H5Aread_helper_STRING’: H5A.c:202:12: warning: unused variable ‘herr’ [-Wunused-variable] 202 | herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR ); | ^~~~ H5A.c:209:12: warning: unused variable ‘herr’ [-Wunused-variable] 209 | herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5D.c -o H5D.o H5D.c: In function ‘H5Dread_helper_INTEGER’: H5D.c:154:20: warning: unused variable ‘status’ [-Wunused-variable] 154 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:151:18: warning: unused variable ‘status’ [-Wunused-variable] 151 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_UCHAR); | ^~~~~~ H5D.c:166:16: warning: unused variable ‘herr’ [-Wunused-variable] 166 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf ); | ^~~~ H5D.c:179:20: warning: unused variable ‘status’ [-Wunused-variable] 179 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:176:18: warning: unused variable ‘status’ [-Wunused-variable] 176 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32); | ^~~~~~ H5D.c:190:16: warning: unused variable ‘herr’ [-Wunused-variable] 190 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf ); | ^~~~ H5D.c:208:24: warning: unused variable ‘status’ [-Wunused-variable] 208 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:205:20: warning: unused variable ‘status’ [-Wunused-variable] 205 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32); | ^~~~~~ H5D.c:220:16: warning: unused variable ‘herr’ [-Wunused-variable] 220 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf ); | ^~~~ H5D.c:254:24: warning: unused variable ‘status’ [-Wunused-variable] 254 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:251:20: warning: unused variable ‘status’ [-Wunused-variable] 251 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative); | ^~~~~~ H5D.c:259:16: warning: unused variable ‘herr’ [-Wunused-variable] 259 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, intbuf ); | ^~~~ H5D.c: In function ‘H5Dread_helper_FLOAT’: H5D.c:410:20: warning: unused variable ‘status’ [-Wunused-variable] 410 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:407:16: warning: unused variable ‘status’ [-Wunused-variable] 407 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_ENUM’: H5D.c:518:20: warning: unused variable ‘status’ [-Wunused-variable] 518 | herr_t status = H5Tenum_insert (enumtype, st, &i); | ^~~~~~ H5D.c:528:24: warning: unused variable ‘status’ [-Wunused-variable] 528 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:525:20: warning: unused variable ‘status’ [-Wunused-variable] 525 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_ARRAY’: H5D.c:606:24: warning: unused variable ‘status’ [-Wunused-variable] 606 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:603:20: warning: unused variable ‘status’ [-Wunused-variable] 603 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_COMPOUND’: H5D.c:712:11: warning: unused variable ‘mem_type_id’ [-Wunused-variable] 712 | hid_t mem_type_id = -1; | ^~~~~~~~~~~ H5D.c: In function ‘H5Dread_helper’: H5D.c:834:12: warning: unused variable ‘status’ [-Wunused-variable] 834 | herr_t status = H5Tclose(dtype_id); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_INTEGER’: H5D.c:366:59: warning: ‘intbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 366 | if (((unsigned long long *)intbuf)[i] > LLONG_MAX) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ H5D.c:253:38: warning: ‘dtypeNative’ may be used uninitialized in this function [-Wmaybe-uninitialized] 253 | hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5D.c: In function ‘H5Dread_helper_ARRAY’: H5D.c:628:23: warning: ‘buf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 628 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5D.c:662:39: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 662 | INTEGER(buffer)[li] = INTEGER(Rval)[lj]; | ^~~~~~~~~~~~~ H5D.c:605:38: warning: ‘arraytype’ may be used uninitialized in this function [-Wmaybe-uninitialized] 605 | hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(arraytype)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5E.c -o H5E.o In file included from /home/biocbuild/bbs-3.13-bioc/R/include/R.h:86, from H5E.h:4, from H5E.c:1: H5E.c: In function ‘custom_print_cb’: /home/biocbuild/bbs-3.13-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label] 52 | #define error Rf_error | ^~~~~~~~ H5E.c:66:5: note: in expansion of macro ‘error’ 66 | error: | ^~~~~ H5E.c: In function ‘custom_print_cb_compact’: /home/biocbuild/bbs-3.13-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label] 52 | #define error Rf_error | ^~~~~~~~ H5E.c:98:5: note: in expansion of macro ‘error’ 98 | error: | ^~~~~ H5E.c:75:15: warning: unused variable ‘indent’ [-Wunused-variable] 75 | const int indent = 4; | ^~~~~~ H5E.c: In function ‘_rhdf5PrintErrorR’: H5E.c:110:16: warning: unused variable ‘eee’ [-Wunused-variable] 110 | herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data); | ^~~ H5E.c: In function ‘_rhdf5PrintErrorRcompact’: H5E.c:141:16: warning: unused variable ‘eee’ [-Wunused-variable] 141 | herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data); | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5G.c -o H5G.o H5G.c: In function ‘_H5Gget_info’: H5G.c:68:10: warning: unused variable ‘herr’ [-Wunused-variable] 68 | herr_t herr = H5Gget_info( group_id, &group_info ); | ^~~~ H5G.c: In function ‘_H5Gget_info_by_name’: H5G.c:116:10: warning: unused variable ‘herr’ [-Wunused-variable] 116 | herr_t herr = H5Gget_info_by_name( loc_id, group_name, &group_info, H5P_DEFAULT ); | ^~~~ H5G.c: In function ‘_H5Gget_info_by_idx’: H5G.c:167:10: warning: unused variable ‘herr’ [-Wunused-variable] 167 | herr_t herr = H5Gget_info_by_idx( loc_id, group_name, index_type, order, n, &group_info, H5P_DEFAULT ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5O.c -o H5O.o H5O.c: In function ‘H5Oget_num_attrs’: H5O.c:13:10: warning: unused variable ‘herr’ [-Wunused-variable] 13 | herr_t herr = H5Aiterate( obj_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &opAcount, &n); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o H5S.c: In function ‘_H5Sselect_hyperslab’: H5S.c:258:12: warning: unused variable ‘herr’ [-Wunused-variable] 258 | herr_t herr = H5Sselect_hyperslab( space_id, op, start, stride, count, block ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S_extras.c -o H5S_extras.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5Z.c -o H5Z.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o HandleListWrap.c: In function ‘_h5listOpenObjects’: HandleListWrap.c:138:12: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 138 | herr_t status; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c external_filters.c -o external_filters.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o h5dump.c: In function ‘opAddToDumpTree’: h5dump.c:68:29: warning: unused variable ‘idx’ [-Wunused-variable] 68 | hsize_t idx=0; | ^~~ h5dump.c: In function ‘_h5dump’: h5dump.c:245:12: warning: unused variable ‘herr’ [-Wunused-variable] 245 | herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToDumpTree, &data ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o h5ls.c: In function ‘opAddToObjList’: h5ls.c:58:29: warning: unused variable ‘idx’ [-Wunused-variable] 58 | hsize_t idx=0; | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5testLock.c -o h5testLock.o h5testLock.c: In function ‘_h5fileLock’: h5testLock.c:9:7: warning: variable ‘lk2’ set but not used [-Wunused-but-set-variable] 9 | int lk2 = -1; | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c printdatatype.c -o printdatatype.o printdatatype.c: In function ‘getDatatypeName’: printdatatype.c:21:16: warning: variable ‘sign_s’ set but not used [-Wunused-but-set-variable] 21 | const char *sign_s=NULL; /* sign scheme string */ | ^~~~~~ printdatatype.c:19:16: warning: variable ‘order_s’ set but not used [-Wunused-but-set-variable] 19 | const char *order_s=NULL; /* byte order string */ | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c wrap.c -o wrap.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-rhdf5/00new/rhdf5/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 (rhdf5)
rhdf5.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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(rhdf5) > > test_check("rhdf5") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 818 ] > > proc.time() user system elapsed 4.933 2.246 9.903
rhdf5.Rcheck/rhdf5-Ex.timings
name | user | system | elapsed | |
H5 | 0.002 | 0.000 | 0.002 | |
H5A | 0.024 | 0.000 | 0.023 | |
H5D | 0.016 | 0.006 | 0.023 | |
H5F | 0.005 | 0.001 | 0.005 | |
H5G | 0.004 | 0.001 | 0.004 | |
H5I | 0.011 | 0.003 | 0.013 | |
H5IdComponent-class | 0.001 | 0.000 | 0.001 | |
H5L | 0.004 | 0.001 | 0.004 | |
H5O | 0.010 | 0.002 | 0.013 | |
H5P | 0.001 | 0.000 | 0.002 | |
H5P_DATASET_ACCESS | 0.000 | 0.000 | 0.001 | |
H5P_DATASET_CREATE | 0.003 | 0.000 | 0.004 | |
H5P_FILE_ACCESS | 0.001 | 0.000 | 0.001 | |
H5P_LINK_CREATE | 0.002 | 0.000 | 0.002 | |
H5S | 0.001 | 0.000 | 0.002 | |
H5T | 0.000 | 0.002 | 0.002 | |
h5closeAll | 0.000 | 0.005 | 0.005 | |
h5const | 0.000 | 0.001 | 0.000 | |
h5createAttribute | 0.008 | 0.002 | 0.010 | |
h5createDataset | 0.040 | 0.004 | 0.048 | |
h5createFile | 0.003 | 0.004 | 0.007 | |
h5createGroup | 0.003 | 0.003 | 0.007 | |
h5errorHandling | 0.000 | 0.000 | 0.001 | |
h5fileLocking | 0.001 | 0.000 | 0.001 | |
h5listIdentifier | 0.004 | 0.000 | 0.004 | |
h5ls | 0.013 | 0.007 | 0.020 | |
h5save | 0.020 | 0.004 | 0.023 | |
h5set_extent | 0.008 | 0.004 | 0.012 | |
h5version | 0.003 | 0.000 | 0.002 | |
h5write | 0.023 | 0.005 | 0.027 | |
rhdf5 | 0.032 | 0.000 | 0.033 | |