Question

我正在尝试为oncotator 1.9.5.0安装ngslib python包。但每次安装因某种原因失败（如下所述）。我尝试过所有可能的方法，比如

pip install ngslib

直接或

python -m pip install --upgrade pip
pip install ngslib

或

git clone https://github.com/tsznxx/ngslib

每次我收到以下错误：

Collecting ngslib
Using cached ngslib-1.1.20.tar.gz
Complete output from command python setup.py egg_info:
Compile KentLib ...
cd lib && make
make[1]: Entering directory `/tmp/pip-build-d1JyTR/ngslib/external/KentLib/lib'
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 chainToPsl.c -o chainToPsl.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 vGfx.c -o vGfx.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 psPoly.c -o psPoly.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 obscure.c -o obscure.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgTimes14.c -o mgTimes14.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 fuzzyShow.c -o fuzzyShow.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 sqlList.c -o sqlList.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 seqOut.c -o seqOut.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 verbose.c -o verbose.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 memgfx.c -o memgfx.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 tabRow.c -o tabRow.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 phyloTree.c -o phyloTree.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 servmsII.c -o servmsII.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 vPng.c -o vPng.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 servcl.c -o servcl.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 xa.c -o xa.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgTimes12.c -o mgTimes12.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 hmmstats.c -o hmmstats.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgTimes8.c -o mgTimes8.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 bwgQuery.c -o bwgQuery.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 numObscure.c -o numObscure.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 jpegSize.c -o jpegSize.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 rbTree.c -o rbTree.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 seqStats.c -o seqStats.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 axt.c -o axt.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 chain.c -o chain.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 chainBlock.c -o chainBlock.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 snof.c -o snof.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 snofmake.c -o snofmake.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 ffAli.c -o ffAli.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgHelvetica10.c -o mgHelvetica10.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 rnautil.c -o rnautil.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 seg.c -o seg.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 htmlPage.c -o htmlPage.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 gemfont.c -o gemfont.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 peakCluster.c -o peakCluster.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 repMask.c -o repMask.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 gff3.c -o gff3.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 apacheLog.c -o apacheLog.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 dnaseq.c -o dnaseq.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 twoBit.c -o twoBit.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 diGraph.c -o diGraph.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgCourier8.c -o mgCourier8.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 aliType.c -o aliType.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 spacedColumn.c -o spacedColumn.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 cirTree.c -o cirTree.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 sqlNum.c -o sqlNum.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 splatAli.c -o splatAli.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 hash.c -o hash.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 snofsig.c -o snofsig.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 gfNet.c -o gfNet.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgHelvetica14.c -o mgHelvetica14.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 boxLump.c -o boxLump.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 fixColor.c -o fixColor.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 linefile.c -o linefile.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 md5.c -o md5.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 dlist.c -o dlist.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 jointalign.c -o jointalign.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 bPlusTree.c -o bPlusTree.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 trix.c -o trix.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgCourier18.c -o mgCourier18.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 rangeTree.c -o rangeTree.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 itsa.c -o itsa.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgHelvetica34.c -o mgHelvetica34.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mafFromAxt.c -o mafFromAxt.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgSixhi6.c -o mgSixhi6.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 kxTok.c -o kxTok.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 pslGenoShow.c -o pslGenoShow.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 spacedSeed.c -o spacedSeed.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 options.c -o options.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 oldGff.c -o oldGff.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 servcis.c -o servcis.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 mgHelveticaBold34.c -o mgHelveticaBold34.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 psGfx.c -o psGfx.o
gcc -c -fPIC -Wall -I../inc  -DMACHTYPE_x86_64 pngwrite.c -o pngwrite.o
pngwrite.c:7:87: error: png.h: No such file or directory
pngwrite.c:13: error: expected ‘)’ before ‘png’
pngwrite.c:19: error: expected ‘)’ before ‘png’
pngwrite.c: In function ‘mgSaveToPng’:
pngwrite.c:34: error: ‘png_structp’ undeclared (first use in this function)
pngwrite.c:34: error: (Each undeclared identifier is reported only once
pngwrite.c:34: error: for each function it appears in.)
pngwrite.c:34: error: expected ‘;’ before ‘png’
pngwrite.c:37: error: ‘png’ undeclared (first use in this function)
pngwrite.c:42: error: ‘png_infop’ undeclared (first use in this function)
pngwrite.c:42: error: expected ‘;’ before ‘info’
pngwrite.c:43: error: ‘info’ undeclared (first use in this function)
pngwrite.c:46: warning: implicit declaration of function ‘png_destroy_write_struct’
pngwrite.c:52: warning: implicit declaration of function ‘png_jmpbuf’
pngwrite.c:62: warning: implicit declaration of function ‘png_init_io’
pngwrite.c:68: warning: implicit declaration of function ‘png_set_IHDR’
pngwrite.c:69: error: ‘PNG_COLOR_TYPE_PALETTE’ undeclared (first use in this function)
pngwrite.c:69: error: ‘PNG_INTERLACE_NONE’ undeclared (first use in this function)
pngwrite.c:70: error: ‘PNG_COMPRESSION_TYPE_DEFAULT’ undeclared (first use in this function)
pngwrite.c:70: error: ‘PNG_FILTER_TYPE_DEFAULT’ undeclared (first use in this function)
pngwrite.c:71: warning: implicit declaration of function ‘png_set_PLTE’
pngwrite.c:72: error: ‘png_color’ undeclared (first use in this function)
pngwrite.c:72: error: expected expression before ‘)’ token
pngwrite.c:80: error: ‘png_byte’ undeclared (first use in this function)
pngwrite.c:80: error: expected ‘;’ before ‘opacities’
pngwrite.c:81: error: ‘opacities’ undeclared (first use in this function)
pngwrite.c:82: error: ‘png_color_16p’ undeclared (first use in this function)
pngwrite.c:82: error: expected ‘;’ before ‘nonPalette_opacities_values’
pngwrite.c:83: warning: implicit declaration of function ‘png_set_tRNS’
pngwrite.c:83: error: ‘nonPalette_opacities_values’ undeclared (first use in this function)
pngwrite.c:91: error: ‘row_pointers’ undeclared (first use in this function)
pngwrite.c:91: error: expected expression before ‘)’ token
pngwrite.c:95: warning: implicit declaration of function ‘png_set_rows’
pngwrite.c:96: warning: implicit declaration of function ‘png_write_png’
pngwrite.c:96: error: ‘PNG_TRANSFORM_IDENTITY’ undeclared (first use in this function)
make[1]: *** [pngwrite.o] Error 1
make[1]: Leaving directory `/tmp/pip-build-d1JyTR/ngslib/external/KentLib/lib'
make: *** [all] Error 2
['-c', 'egg_info', '--egg-base', 'pip-egg-info']
ERROR: Compiling KentLib error!

----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in  /tmp/pip-  build-d1JyTR/ngslib/

最初它开始很好，但后来setup.py出现错误。 大部分时间都在png.h档案。

如何为oncotator安装ngslib（特别是1.1.9）（用于注释目的的包）？我正在使用oracle Linux服务器并使用python 2.7

感谢。

Answer 1

您是否也安装了正确的依赖项？

根据github，您需要安装numpy和pysam并且argparse会自动包含在python2.7 +

中

此外这是一个共享的Linux服务器，如果是这样你可能只是缺乏安装权限，在这种情况下你应该使用virtualenv或pyenv为你的python安装本地虚拟环境。

Answer 2

如果是该文件，则可能是您没有gcc编译器

NGSLIB包装安装出错

2 个答案: