Travel.install - Githubissues

Yikun commented 1 year ago
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Travel
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Travel’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Cpp_interface.cpp -o Cpp_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c altfile_operations.cpp -o altfile_operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c altmmap_operations.cpp -o altmmap_operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c altrep_manager.cpp -o altrep_manager.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c class_Cache_block.cpp -o class_Cache_block.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c class_Filesystem_cache_copier.cpp -o class_Filesystem_cache_copier.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `pkg-config fuse --cflags` -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c class_Filesystem_file_data.cpp -o class_Filesystem_file_data.o
In file included from class_Filesystem_file_data.h:5,
                 from class_Filesystem_file_data.cpp:1:
class_Cache_block.h:10:5: error: ‘size_t’ does not name a type
   10 |     size_t size;
      |     ^~~~~~
class_Cache_block.h:1:1: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
  +++ |+#include <cstddef>
    1 | #ifndef HEADER_CACHE_BLOCK
class_Cache_block.h:11:5: error: ‘size_t’ does not name a type
   11 |     size_t *counter = nullptr;
      |     ^~~~~~
class_Cache_block.h:11:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:14:23: error: expected ‘)’ before ‘size’
   14 |     Cache_block(size_t size);
      |                ~      ^~~~~
      |                       )
class_Cache_block.h:21:5: error: ‘size_t’ does not name a type
   21 |     size_t use_count() const;
      |     ^~~~~~
class_Cache_block.h:21:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:23:5: error: ‘size_t’ does not name a type
   23 |     size_t get_size() const;
      |     ^~~~~~
class_Cache_block.h:23:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:27:5: error: ‘size_t’ does not name a type
   27 |     size_t get_serialize_size() const;
      |     ^~~~~~
class_Cache_block.h:27:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Filesystem_file_data.cpp: In member function ‘size_t Filesystem_file_data::get_serialize_size()’:
class_Filesystem_file_data.cpp:70:26: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   70 |         size += i.second.get_serialize_size();
      |                          ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_file_data::serialize(void*)’:
class_Filesystem_file_data.cpp:92:39: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   92 |         size_t buffer_size = i.second.get_serialize_size();
      |                                       ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_cache_index_iterator::compute_block_info()’:
class_Filesystem_file_data.cpp:177:39: error: ‘class Cache_block’ has no member named ‘get_size’
  177 |     block_length = block_iter->second.get_size() / type_size;
      |                                       ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: class_Filesystem_file_data.o] Error 1
ERROR: compilation failed for package ‘Travel’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Travel’
martin-g commented 1 year ago
Fails on x86_64 too - https://bioconductor.org/checkResults/3.17/bioc-LATEST/Travel/nebbiolo1-install.html
martin-g commented 1 year ago
Reported upstream with https://github.com/Jiefei-Wang/Travel/issues/1
martin-g commented 1 year ago
PR: https://github.com/Jiefei-Wang/Travel/pull/2
martin-g commented 1 year ago
https://bioconductor.org/checkResults/3.18/bioc-LATEST/Travel/kunpeng2-buildsrc.html is OK only on Kunpeng2! But the package is deprecated and will be removed for 3.19
Yikun / BBS

Travel.install #27
