It is a pitty this package is not available at all for amd64. I went to check why and at least RNAfold works anyway. I will contact the author about the problems shown below. Compiling readseq... x86_64-pc-linux-gnu-gcc -O2 -march=nocona -fomit-frame-pointer -pipe -o readseq readseq.c ureadseq.c readseq.c: In function 'formatstr': readseq.c:261: warning: return discards qualifiers from pointer target type readseq.c:263: warning: return discards qualifiers from pointer target type readseq.c:267: warning: return discards qualifiers from pointer target type ureadseq.c: In function 'addseq': ureadseq.c:158: warning: cast to pointer from integer of different size ureadseq.c: In function 'compressSeq': ureadseq.c:1542: warning: cast to pointer from integer of different size /var/tmp/portage/sci-biology/vienna-rna-1.6.5/temp/ccYhOtgd.o: In function `main': readseq.c:(.text+0x13ea): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /var/tmp/portage/sci-biology/vienna-rna-1.6.5/temp/ccYhOtgd.o: In function `chooseFormat': readseq.c:(.text+0x846): warning: the `gets' function is dangerous and should not be used. Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff test.alpha alphabet.std 1c1 < >alphabet['!'..'~'], 83 bases, E14ECBE2 checksum. --- > >alphabet['!'..'~'], 83 bases, 9429 checksum. make: [test] Error 1 (ignored) Test for valid format conversions: ./readseq -v -p -f=ig nucleic.std -otest.ig readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino test ./readseq -v -p -f=gb test.ig -otest.gb readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino ./readseq -v -p -f=nbrf test.gb -otest.nbrf readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp ./readseq -v -p -f=embl test.nbrf -otest.embl readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino ./readseq -v -p -f=gcg test.embl -otest.gcg readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino ./readseq -v -p -f=strider test.gcg -otest.strider readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino ./readseq -v -p -f=fitch test.strider -otest.fitch readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=fasta test.fitch -otest.fasta readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=pir test.fasta -otest.pir readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=ig test.pir -otest.ig-b readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, diff test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, make: [test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss make: [test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean >>> Source compiled.
From: Ivo Hofacker (author of RNA Vienna package) Dear Martin, As far as I can see readseq works fine, the test is just not done very well. As the message says " Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem." The checksums are indeed ok, there are only whitespace differences in the header lines. In other words all test cases work, and the test should return success. The readseq program is not written by us, and therefore I don't want to make a lot of changes to it. As far as I know it's also no longer supported by the original author (there's a newer version in java). It's not an essential part of the package, but since it's useful to some people and we still distribute it. Best wishes, Ivo
Hi Martin, Thanks much for your note. Unfortunately, it is not uncommon that the "testing" part of packages (if they exist at all) is being neglected. Hence, failing tests often just mean that the tests are broken, not the package itself. Since upstream won't fix the tests we'll probably have to live with them failing as long as vienna-rna does what is is supposed to do. Best, Markus
Since upstream won't deal with the tests and the package itself seems to work I am closing this as CANTFIX. Thanks, Markus
