samblaster install throws warnings when building docker image.

[asifzubair]

Step 7 : RUN bash /tmp/install_samblaster.sh
 ---> Running in 700e73309e63
Cloning into 'samblaster'...
g++ -Wall -O3 -D BUILDNUM=22 -c samblaster.cpp -o samblaster.o
samblaster.cpp: In function 'void fsError(const char*)':
samblaster.cpp:63:77: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
         asprintf(&temp, "samblaster: File '%s' does not exist.\n", filename);
                                                                             ^
samblaster.cpp:65:87: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
         asprintf(&temp, "samblaster: File system error on %s: %d.\n", filename, errno);
                                                                                       ^
samblaster.cpp: In function 'void brokenBlock(splitLine_t*, int)':
samblaster.cpp:777:103: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
              count, block->fields[QNAME], "samblaster: Are you sure the input is sorted by read ids?");
                                                                                                       ^
samblaster.cpp: In function 'int main(int, char**)':
samblaster.cpp:1347:111: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
         asprintf(&temp, "samblaster: Invalid minimum non overlap parameter given: %d\n", state->minNonOverlap);
                                                                                                               ^
samblaster.cpp:1353:111: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
         asprintf(&temp, "samblaster: Invalid maximum split count parameter given: %d\n", state->maxSplitCount);
                                                                                                               ^
g++ -Wall -O3 -D BUILDNUM=22 -c sbhash.cpp -o sbhash.o
sbhash.cpp: In function 'void checkFSerrWithFilename(ssize_t)':
sbhash.cpp:45:95: warning: ignoring return value of 'int asprintf(char**, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
             asprintf(&temp, "File system error %d trying to allocate or free memory\n", errno);
                                                                                               ^
g++  -o samblaster samblaster.o sbhash.o
 ---> 3e90a8ce946d
Removing intermediate container 700e73309e63
Successfully built 3e90a8ce946d

[ttriche]

these look like warnings rather than errors. Does the samblaster binary build? The -Wall flag is designed to cause GCC to flag everything it can, including stylistic or dead-code warnings.

Statistics is the grammar of science. Karl Pearson http://en.wikipedia.org/wiki/The_Grammar_of_Science

On Wed, Jul 15, 2015 at 5:34 PM, Asif Zubair notifications@github.com wrote:

Cloning into 'samblaster'... g++ -Wall -O3 -D BUILDNUM=22 -c samblaster.cpp -o samblaster.o samblaster.cpp: In function 'void fsError(const char_)': samblaster.cpp:63:77: warning: ignoring return value of 'int asprintf(char_, const char, ...)', declared with attribute warn_unusedresult [-Wunused-result] asprintf(&temp, "samblaster: File '%s' does not exist.\n", filename); ^ samblaster.cpp:65:87: warning: ignoring return value of 'int asprintf(char**, const char, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&temp, "samblaster: File system error on %s: %d.\n", filename, errno); ^ samblaster.cpp: In function 'void brokenBlock(splitLinet, int)': samblaster.cpp:777:103: warning: ignoring return value of 'int asprintf(char, const char_, ...)', declared with attribute warn_unusedresult [-Wunused-result] count, block->fields[QNAME], "samblaster: Are you sure the input is sorted by read ids?"); ^ samblaster.cpp: In function 'int main(int, char)': samblaster.cpp:1347:111: warning: ignoring return value of 'int asprintf(char, const char, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&temp, "samblaster: Invalid minimum non overlap parameter given: %d\n", state->minNonOverlap); ^ samblaster.cpp:1353:111: warning: ignoring return value of 'int asprintf(char, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&temp, "samblaster: Invalid maximum split count parameter given: %d\n", state->maxSplitCount); ^ g++ -Wall -O3 -D BUILDNUM=22 -c sbhash.cpp -o sbhash.o sbhash.cpp: In function 'void checkFSerrWithFilename(ssize_t)': sbhash.cpp:45:95: warning: ignoring return value of 'int asprintf(char*, const char, ...)', declared with attribute warn_unused_result [-Wunused-result] asprintf(&temp, "File system error %d trying to allocate or free memory\n", errno); ^ g++ -o samblaster samblaster.o sbhash.o

— Reply to this email directly or view it on GitHub https://github.com/RamsinghLab/atacseq_counts/issues/2.

[asifzubair]

Yes, the binary gets built and I checked by running samblaster in the container.

[ttriche]

Ok, probably would be a good idea to close this issue then.

[asifzubair]

Sure. Posting the logs here for sake of book-keeping. thanks!