Mike Jiang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RProtoBufLib |
| Branch: RELEASE_3_9 |
| Last Commit: 899b78e |
| Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:38:46 -0400 (Wed, 16 Oct 2019).
| Package 1412/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RProtoBufLib 1.6.0 Mike Jiang
| 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 | |
| Package: RProtoBufLib |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RProtoBufLib.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RProtoBufLib_1.6.0.tar.gz |
| StartedAt: 2019-10-16 06:46:26 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:47:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 43.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RProtoBufLib.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RProtoBufLib.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RProtoBufLib_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RProtoBufLib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RProtoBufLib' version '1.6.0'
* 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 'RProtoBufLib' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
include 1.3Mb
lib 4.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
BSD_3_clause
* 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 ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/RProtoBufLib/libs/i386/RProtoBufLib.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/RProtoBufLib/libs/x64/RProtoBufLib.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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
'UsingRProtoBufLib.Rmd'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.Rcheck/00check.log'
for details.
RProtoBufLib.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/RProtoBufLib_1.6.0.tar.gz && rm -rf RProtoBufLib.buildbin-libdir && mkdir RProtoBufLib.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RProtoBufLib.buildbin-libdir RProtoBufLib_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RProtoBufLib_1.6.0.zip && rm RProtoBufLib_1.6.0.tar.gz RProtoBufLib_1.6.0.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
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
5 1968k 5 112k 0 0 39818 0 0:00:50 0:00:02 0:00:48 39947
91 1968k 91 1792k 0 0 458k 0 0:00:04 0:00:03 0:00:01 459k
100 1968k 100 1968k 0 0 503k 0 0:00:03 0:00:03 --:--:-- 504k
install for i386
* installing *source* package 'RProtoBufLib' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/ -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
In file included from GatingSet_pb_lib/GatingSet.pb.cc:12:0:
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)7u]':
win/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = long long unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)6u]':
win/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)15u]':
win/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = long long int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)16u]':
win/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = float; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)2u]':
win/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = double; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)1u]':
win/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
mkdir -p ""C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include""
cp -r win/include/google "C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386"
cp win/lib/i386/libprotobuf.a "C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386/libprotobuf.a"
cp GatingSet_pb_lib/GatingSet.pb.o C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/i386/GatingSet.pb.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/ -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dummy.cpp -o dummy.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.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/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RProtoBufLib'
finding HTML links ... done
LdFlags 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 'RProtoBufLib' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/ -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GatingSet_pb_lib/GatingSet.pb.cc -o GatingSet_pb_lib/GatingSet.pb.o
In file included from GatingSet_pb_lib/GatingSet.pb.cc:12:0:
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)7u]':
win/include/google/protobuf/wire_format_lite_inl.h:413:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = long long unsigned int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)6u]':
win/include/google/protobuf/wire_format_lite_inl.h:414:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)15u]':
win/include/google/protobuf/wire_format_lite_inl.h:415:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = long long int; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)16u]':
win/include/google/protobuf/wire_format_lite_inl.h:416:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = float; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)2u]':
win/include/google/protobuf/wire_format_lite_inl.h:417:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h: In instantiation of 'static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField*) [with CType = double; google::protobuf::internal::WireFormatLite::FieldType DeclaredType = (google::protobuf::internal::WireFormatLite::FieldType)1u]':
win/include/google/protobuf/wire_format_lite_inl.h:418:1: required from here
win/include/google/protobuf/wire_format_lite_inl.h:383:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
win/include/google/protobuf/wire_format_lite_inl.h:393:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < new_entries; ++i) {
^
mkdir -p ""C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include""
cp -r win/include/google "C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/include"
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64"
cp win/lib/x64/libprotobuf.a "C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64/libprotobuf.a"
cp GatingSet_pb_lib/GatingSet.pb.o C:/Users/biocbuild/bbs-3.9-bioc/meat/RProtoBufLib.buildbin-libdir/RProtoBufLib/lib/x64/GatingSet.pb.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I../inst/include/ -Iwin/include/ -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c dummy.cpp -o dummy.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o RProtoBufLib.dll tmp.def dummy.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/RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RProtoBufLib' as RProtoBufLib_1.6.0.zip
* DONE (RProtoBufLib)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RProtoBufLib' successfully unpacked and MD5 sums checked
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RProtoBufLib.Rcheck/examples_i386/RProtoBufLib-Ex.timings
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RProtoBufLib.Rcheck/examples_x64/RProtoBufLib-Ex.timings
|