Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for rhdf5 on malbec2

This page was generated on 2019-04-09 11:31:48 -0400 (Tue, 09 Apr 2019).

Package 1344/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5 2.27.15
Mike Smith
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/rhdf5
Branch: master
Last Commit: 65e4add
Last Changed Date: 2019-03-11 05:39:26 -0400 (Mon, 11 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: rhdf5
Version: 2.27.15
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rhdf5_2.27.15.tar.gz
StartedAt: 2019-04-09 03:12:47 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:15:40 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 172.7 seconds
RetCode: 0
Status:  OK 
CheckDir: rhdf5.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rhdf5_2.27.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rhdf5.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 ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.27.15’
* 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 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/rhdf5.Rcheck/00check.log’
for details.

Installation output

rhdf5.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rhdf5
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘rhdf5’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5.c -o H5.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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:166:10: warning: unused variable ‘herr’ [-Wunused-variable]
   herr_t herr = H5Aread(attr_id, mem_type_id, buf );
          ^˜˜˜
H5A.c: In function ‘H5Aread_helper_FLOAT’:
H5A.c:199:10: warning: unused variable ‘herr’ [-Wunused-variable]
   herr_t herr = H5Aread(attr_id, mem_type_id, buf );
          ^˜˜˜
H5A.c: In function ‘H5Aread_helper_STRING’:
H5A.c:226:12: warning: unused variable ‘herr’ [-Wunused-variable]
     herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
            ^˜˜˜
H5A.c:233:12: warning: unused variable ‘herr’ [-Wunused-variable]
     herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
            ^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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:276:24: warning: unused variable ‘status’ [-Wunused-variable]
                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                        ^˜˜˜˜˜
H5D.c:273:20: warning: unused variable ‘status’ [-Wunused-variable]
             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
                    ^˜˜˜˜˜
H5D.c:288:16: warning: unused variable ‘herr’ [-Wunused-variable]
         herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
                ^˜˜˜
H5D.c:328:24: warning: unused variable ‘status’ [-Wunused-variable]
                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                        ^˜˜˜˜˜
H5D.c:325:20: warning: unused variable ‘status’ [-Wunused-variable]
             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
                    ^˜˜˜˜˜
H5D.c:333:16: warning: unused variable ‘herr’ [-Wunused-variable]
         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:499:20: warning: unused variable ‘status’ [-Wunused-variable]
             herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                    ^˜˜˜˜˜
H5D.c:496:16: warning: unused variable ‘status’ [-Wunused-variable]
         herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
                ^˜˜˜˜˜
H5D.c:512:12: warning: unused variable ‘herr’ [-Wunused-variable]
     herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
            ^˜˜˜
H5D.c: In function ‘H5Dread_helper_STRING’:
H5D.c:538:20: warning: unused variable ‘status’ [-Wunused-variable]
             herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                    ^˜˜˜˜˜
H5D.c:535:16: warning: unused variable ‘status’ [-Wunused-variable]
         herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtype_id);
                ^˜˜˜˜˜
H5D.c:547:18: warning: unused variable ‘herr’ [-Wunused-variable]
           herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, bufSTR );
                  ^˜˜˜
H5D.c:557:18: warning: unused variable ‘herr’ [-Wunused-variable]
           herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, bufSTR );
                  ^˜˜˜
H5D.c: In function ‘H5Dread_helper_ENUM’:
H5D.c:593:20: warning: unused variable ‘status’ [-Wunused-variable]
             herr_t status = H5Tenum_insert (enumtype, st, &i);
                    ^˜˜˜˜˜
H5D.c:604:24: warning: unused variable ‘status’ [-Wunused-variable]
                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                        ^˜˜˜˜˜
H5D.c:601:20: warning: unused variable ‘status’ [-Wunused-variable]
             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
                    ^˜˜˜˜˜
H5D.c:619:16: warning: unused variable ‘herr’ [-Wunused-variable]
         herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
                ^˜˜˜
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:679:24: warning: unused variable ‘status’ [-Wunused-variable]
                 herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                        ^˜˜˜˜˜
H5D.c:676:20: warning: unused variable ‘status’ [-Wunused-variable]
             herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
                    ^˜˜˜˜˜
H5D.c:701:16: warning: unused variable ‘herr’ [-Wunused-variable]
         herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
                ^˜˜˜
H5D.c: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:782:11: warning: unused variable ‘mem_type_id’ [-Wunused-variable]
     hid_t mem_type_id = -1;
           ^˜˜˜˜˜˜˜˜˜˜
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:448:59: warning: ‘intbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                         if (((unsigned long long *)intbuf)[i] > LLONG_MAX) {
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
H5D.c:327:38: warning: ‘dtypeNative’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative));
                                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:701:16: warning: ‘buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
                ^˜˜˜
H5D.c:732:39: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 INTEGER(buffer)[li] = INTEGER(Rval)[lj];
                                       ^˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:678:38: warning: ‘arraytype’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                 hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(arraytype));
                                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include/R.h:86:0,
                 from H5E.h:4,
                 from H5E.c:1:
H5E.c: In function ‘custom_print_cb’:
/home/biocbuild/bbs-3.9-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label]
 #define error Rf_error
               ^
H5E.c:76:3: note: in expansion of macro ‘error’
   error:
   ^˜˜˜˜
H5E.c: In function ‘custom_print_cb_compact’:
/home/biocbuild/bbs-3.9-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label]
 #define error Rf_error
               ^
H5E.c:112:3: note: in expansion of macro ‘error’
   error:
   ^˜˜˜˜
H5E.c:87:16: warning: unused variable ‘indent’ [-Wunused-variable]
     const int  indent = 4;
                ^˜˜˜˜˜
H5E.c: In function ‘_rhdf5PrintErrorR’:
H5E.c:121:12: warning: unused variable ‘eee’ [-Wunused-variable]
     herr_t eee = H5Ewalk(estack_id, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data);
            ^˜˜
H5E.c: In function ‘_rhdf5PrintErrorRcompact’:
H5E.c:153:12: warning: unused variable ‘eee’ [-Wunused-variable]
     herr_t eee = H5Ewalk(estack_id, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data);
            ^˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5F.c -o H5F.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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]
   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]
   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]
   herr_t herr = H5Gget_info_by_idx( loc_id, group_name, index_type, order, n, &group_info, H5P_DEFAULT );
          ^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5I.c -o H5I.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5L.c -o H5L.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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]
   herr_t herr = H5Aiterate( obj_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &opAcount, &n);
          ^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5P.c -o H5P.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5S.c -o H5S.o
H5S.c: In function ‘_H5Sselect_cols’:
H5S.c:223:10: warning: unused variable ‘j’ [-Wunused-variable]
   int i, j;
          ^
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5T.c -o H5T.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c H5constants.c -o H5constants.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c HandleList.cpp -o HandleList.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c HandleListWrap.c -o HandleListWrap.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c h5dump.c -o h5dump.o
h5dump.c: In function ‘_h5dump’:
h5dump.c:332:12: warning: unused variable ‘herr’ [-Wunused-variable]
     herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToLinfoTree, &data );
            ^˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c h5ls.c -o h5ls.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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]
   int lk2 = -1;
       ^˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-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]
   const char  *sign_s=NULL;   /* sign scheme string */
                ^˜˜˜˜˜
printdatatype.c:19:16: warning: variable ‘order_s’ set but not used [-Wunused-but-set-variable]
   const char  *order_s=NULL;  /* byte order string */
                ^˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c wrap.c -o wrap.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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 H5T.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o wrap.o /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)

Tests output

rhdf5.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(rhdf5)
> 
> test_check("rhdf5")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 668 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.322  19.990 142.940

Example timings

rhdf5.Rcheck/rhdf5-Ex.timings

nameusersystemelapsed
H50.0030.0000.003
H5A0.0240.0040.028
H5D0.030.000.03
H5F0.0060.0000.007
H5G0.0060.0000.006
H5I0.0140.0000.014
H5IdComponent-class0.0010.0000.000
H5L0.0050.0000.006
H5O0.0120.0000.012
H5P0.0020.0000.002
H5P_DATASET_ACCESS0.0020.0000.001
H5P_DATASET_CREATE0.0100.0000.009
H5P_LINK_CREATE0.0030.0000.003
H5S0.0020.0000.002
H5T0.0010.0000.002
h5closeAll0.0070.0000.007
h5const0.0010.0000.001
h5createAttribute0.0130.0000.012
h5createDataset0.0440.0000.044
h5createFile0.0080.0000.008
h5createGroup0.0090.0000.008
h5errorHandling000
h5fileLocking0.0010.0000.001
h5listIdentifier0.0060.0000.005
h5ls0.0230.0000.023
h5save0.0350.0000.034
h5set_extent0.0120.0000.012
h5version0.0020.0000.002
h5write0.0210.0040.025
rhdf50.0270.0000.027