Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 276/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
casper 2.40.0 (landing page) David Rossell
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the casper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/casper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: casper |
Version: 2.40.0 |
Command: /home/biocbuild/R/R/bin/R CMD INSTALL casper |
StartedAt: 2024-11-19 21:16:27 -0000 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 21:18:04 -0000 (Tue, 19 Nov 2024) |
EllapsedTime: 96.8 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL casper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘casper’ ... ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c casper.cpp -o casper.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c cstat.cpp -o cstat.o cstat.cpp: In function 'void free_vector(float*, int, int)': cstat.cpp:1111:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long unsigned int)nl) * 4)))' and NULL [-Waddress] 1111 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function 'void free_dvector(double*, int, int)': cstat.cpp:1117:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long unsigned int)nl) * 8)))' and NULL [-Waddress] 1117 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function 'void free_ivector(int*, int, int)': cstat.cpp:1123:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long unsigned int)nl) * 4)))' and NULL [-Waddress] 1123 | if( (v+nl) != NULL ) free((char *) (v+nl)); | ^ cstat.cpp: In function 'void free_dmatrix(double**, int, int, int, int)': cstat.cpp:1131:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 8)))' and NULL [-Waddress] 1131 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL ) | ^ cstat.cpp:1133:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long unsigned int)nrl) * 8)))' and NULL [-Waddress] 1133 | if( (m+nrl) != NULL ) free((char *) (m+nrl)); | ^ cstat.cpp: In function 'void free_imatrix(int**, int, int, int, int)': cstat.cpp:1141:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long unsigned int)i) * 8)))) + ((sizetype)(((long unsigned int)ncl) * 4)))' and NULL [-Waddress] 1141 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL ) | ^ cstat.cpp:1143:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long unsigned int)nrl) * 8)))' and NULL [-Waddress] 1143 | if( (m+nrl) != NULL ) free((char *) (m+nrl)); | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c dataframe.cpp -o dataframe.o In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/map:62, from variant.h:3, from variant_cmp.h:1, from model.h:1, from model_cmp.h:1, from dataframe.h:1, from dataframe.cpp:2: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_unique_pos(const key_type&) [with _Key = Variant*; _Val = Variant*; _KeyOfValue = std::_Identity<Variant*>; _Compare = VariantCmp; _Alloc = std::allocator<Variant*>]', inlined from 'std::pair<std::_Rb_tree_iterator<_Val>, bool> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique(_Arg&&) [with _Arg = Variant* const&; _Key = Variant*; _Val = Variant*; _KeyOfValue = std::_Identity<Variant*>; _Compare = VariantCmp; _Alloc = std::allocator<Variant*>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_tree.h:2167:28, inlined from 'std::pair<typename std::_Rb_tree<_Key, _Key, std::_Identity<_Tp>, _Compare, typename __gnu_cxx::__alloc_traits<_Alloc>::rebind<_Key>::other>::const_iterator, bool> std::set<_Key, _Compare, _Alloc>::insert(const value_type&) [with _Key = Variant*; _Compare = VariantCmp; _Alloc = std::allocator<Variant*>]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_set.h:514:25, inlined from 'void DataFrame::path2Variants(std::set<Variant*, VariantCmp>*, std::set<Variant*, VariantCmp>*, std::set<std::__cxx11::basic_string<char> >*, bool*, std::set<Variant*, VariantCmp>*, Fragment*)' at dataframe.cpp:598:36: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_tree.h:2114:42: warning: 'bestvar' may be used uninitialized [-Wmaybe-uninitialized] 2114 | __comp = _M_impl._M_key_compare(__k, _S_key(__x)); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ dataframe.cpp: In member function 'void DataFrame::path2Variants(std::set<Variant*, VariantCmp>*, std::set<Variant*, VariantCmp>*, std::set<std::__cxx11::basic_string<char> >*, bool*, std::set<Variant*, VariantCmp>*, Fragment*)': dataframe.cpp:481:12: note: 'bestvar' was declared here 481 | Variant *bestvar; | ^~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c discretedf.cpp -o discretedf.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c dropVariant.cpp -o dropVariant.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c exon.cpp -o exon.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fragFunc.c -o fragFunc.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c fragment.cpp -o fragment.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c functions.c -o functions.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hash.c -o hash.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c join_exons.c -o join_exons.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c makeIslands.c -o makeIslands.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c model.cpp -o model.o model.cpp: In member function 'char* Model::toString()': model.cpp:147:24: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict] 147 | sprintf(str, "%s {%s}", str, vstr); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c model_cmp.cpp -o model_cmp.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c pathCounts.c -o pathCounts.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c procBam.c -o procBam.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c rcasper.cpp -o rcasper.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c seppel.cpp -o seppel.o seppel.cpp: In member function 'void Seppel::exploreUnif(int, std::set<Variant*, VariantCmp>*)': seppel.cpp:484:9: warning: array subscript -1 is outside array bounds of 'void [24]' [-Warray-bounds=] 484 | delete [] possiblemodels; | ^~~~~~~~~~~~~~~~~~~~~~~~ seppel.cpp:402:55: note: at offset -8 into object of size 24 allocated by 'operator new' 402 | vector<Model*>* possiblemodels = new vector<Model*>(); | ^ seppel.cpp:484:19: warning: 'void operator delete [](void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 484 | delete [] possiblemodels; | ^~~~~~~~~~~~~~ seppel.cpp:402:55: note: returned from 'void* operator new(std::size_t)' 402 | vector<Model*>* possiblemodels = new vector<Model*>(); | ^ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c simReads.c -o simReads.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c simReadsfunc.c -o simReadsfunc.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c smartmodeldist.cpp -o smartmodeldist.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c uniqQname.c -o uniqQname.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c variant.cpp -o variant.o variant.cpp: In member function 'void Variant::toString(char*)': variant.cpp:164:52: warning: 'sprintf' argument 3 overlaps destination object 'str' [-Wrestrict] 164 | for (int e = 0; e < exonCount; e++) sprintf(str, "%s,%i", str, exons[e]->id); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ variant.cpp:156:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here 156 | void Variant::toString(char *str) | ~~~~~~^~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c variant_cmp.cpp -o variant_cmp.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o casper.so casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-casper/00new/casper/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘transcripts’ in package ‘casper’ ** 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 (casper)