##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rhdf5.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rhdf5_2.32.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rhdf5.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.32.4’
* 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 ... 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 ... 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 ... 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 ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/rhdf5/libs/rhdf5.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/rhdf5.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rhdf5
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘rhdf5’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5.c -o H5.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5A.c -o H5A.o
H5A.c:142:10: warning: unused variable 'herr' [-Wunused-variable]
  herr_t herr = H5Aread(attr_id, mem_type_id, buf );
         ^
H5A.c:175:10: warning: unused variable 'herr' [-Wunused-variable]
  herr_t herr = H5Aread(attr_id, mem_type_id, buf );
         ^
H5A.c:202:12: warning: unused variable 'herr' [-Wunused-variable]
    herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
           ^
H5A.c:209:12: warning: unused variable 'herr' [-Wunused-variable]
    herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
           ^
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5D.c -o H5D.o
H5D.c:155:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                   ^
H5D.c:152:18: warning: unused variable 'status' [-Wunused-variable]
          herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_UCHAR);
                 ^
H5D.c:167:16: 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:180:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                   ^
H5D.c:177:18: warning: unused variable 'status' [-Wunused-variable]
          herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
                 ^
H5D.c:191:16: 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:209:24: warning: unused variable 'status' [-Wunused-variable]
                herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                       ^
H5D.c:206:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
                   ^
H5D.c:221:16: 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:261:24: warning: unused variable 'status' [-Wunused-variable]
                herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                       ^
H5D.c:258:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
                   ^
H5D.c:266:16: 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:247:20: warning: variable 'intbuf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        } else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:251:13: note: uninitialized use occurs here
        if (intbuf == 0) {
            ^~~~~~
H5D.c:247:16: note: remove the 'if' if its condition is always true
        } else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:237:21: note: initialize the variable 'intbuf' to silence this warning
        void* intbuf;
                    ^
                     = NULL
H5D.c:433:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                   ^
H5D.c:430:16: warning: unused variable 'status' [-Wunused-variable]
        herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
               ^
H5D.c:541:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tenum_insert (enumtype, st, &i);
                   ^
H5D.c:552:24: warning: unused variable 'status' [-Wunused-variable]
                herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                       ^
H5D.c:549:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
                   ^
H5D.c:630:24: warning: unused variable 'status' [-Wunused-variable]
                herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
                       ^
H5D.c:627:20: warning: unused variable 'status' [-Wunused-variable]
            herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
                   ^
H5D.c:646:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            } else if (superclass == H5T_FLOAT) {
                       ^~~~~~~~~~~~~~~~~~~~~~~
H5D.c:652:98: note: uninitialized use occurs here
        herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
                                                                                                 ^~~
H5D.c:646:20: note: remove the 'if' if its condition is always true
            } else if (superclass == H5T_FLOAT) {
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:639:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            } else if (superclass == H5T_FLOAT) {
                       ^~~~~~~~~~~~~~~~~~~~~~~
H5D.c:652:98: note: uninitialized use occurs here
        herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
                                                                                                 ^~~
H5D.c:639:20: note: remove the 'if' if its condition is always true
            } else if (superclass == H5T_FLOAT) {
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:634:19: note: initialize the variable 'buf' to silence this warning
        void * buf;
                  ^
                   = NULL
H5D.c:736:11: warning: unused variable 'mem_type_id' [-Wunused-variable]
    hid_t mem_type_id = -1;
          ^
H5D.c:858:12: warning: unused variable 'status' [-Wunused-variable]
    herr_t status = H5Tclose(dtype_id);
           ^
24 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5E.c -o H5E.o
H5E.c:66:5: warning: unused label 'Rf_error' [-Wunused-label]
    error:
    ^~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
              ^
H5E.c:75:15: warning: unused variable 'indent' [-Wunused-variable]
    const int indent = 4;
              ^
H5E.c:98:5: warning: unused label 'Rf_error' [-Wunused-label]
    error:
    ^~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
              ^
H5E.c:110:16: warning: unused variable 'eee' [-Wunused-variable]
        herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data);
               ^
H5E.c:141:16: warning: unused variable 'eee' [-Wunused-variable]
        herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data);
               ^
5 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5F.c -o H5F.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5G.c -o H5G.o
H5G.c:68:10: warning: unused variable 'herr' [-Wunused-variable]
  herr_t herr = H5Gget_info( group_id, &group_info );
         ^
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: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 );
         ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5I.c -o H5I.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5L.c -o H5L.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5O.c -o H5O.o
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);
         ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5P.c -o H5P.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5S.c -o H5S.o
H5S.c:223:10: warning: unused variable 'j' [-Wunused-variable]
  int i, j;
         ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5T.c -o H5T.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5Z.c -o H5Z.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c H5constants.c -o H5constants.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c HandleList.cpp -o HandleList.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c HandleListWrap.c -o HandleListWrap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5dump.c -o h5dump.o
h5dump.c:301:12: warning: unused variable 'herr' [-Wunused-variable]
    herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToLinfoTree, &data );
           ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5ls.c -o h5ls.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5testLock.c -o h5testLock.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c h5writeDataFrame.c -o h5writeDataFrame.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c printdatatype.c -o printdatatype.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c wrap.c -o wrap.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 H5Z.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 743 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.356   2.616  13.847