vgl-hub / gfastats

A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
MIT License
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issues about install: phmap.h (No such file or directory) #47

Closed maxmaronna closed 6 months ago

maxmaronna commented 6 months ago

Hello, I am having issues to install gfastats in a new server:

(ngs) maxmaronna@access2:~/01-SOFTWARE/gfastats/gfastats$ make -j g++ -g -std=gnu++14 -O3 -I./include -Igfalibs/include -Wall -Wextra -pthread -c src/main.cpp -o build/bin/.o/main g++ -g -std=gnu++14 -O3 -I./include -Igfalibs/include -Wall -Wextra -pthread -c src/input.cpp -o build/bin/.o/input make -j -C /home/maxmaronna/01-SOFTWARE/gfastats/gfastats/gfalibs CXXFLAGS="-g -std=gnu++14 -O3 -I./include -Igfalibs/include -Wall -Wextra " make[1]: Entering directory '/home/maxmaronna/01-SOFTWARE/gfastats/gfastats/gfalibs' make[1]: No targets specified and no makefile found. Stop. make[1]: Leaving directory '/home/maxmaronna/01-SOFTWARE/gfastats/gfastats/gfalibs' make: [Makefile:41: gfalibs] Error 2 make: *** Waiting for unfinished jobs.... src/input.cpp:8:10: fatal error: parallel-hashmap/phmap.h: No such file or directory

include <parallel-hashmap/phmap.h>

      ^~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated. make: *** [Makefile:37: build/bin/.o/input] Error 1 In file included from src/main.cpp:7: ./include/main.h:31:10: fatal error: log.h: No such file or directory

include "log.h"

      ^~~~~~~

compilation terminated. make: *** [Makefile:37: build/bin/.o/main] Error 1

Thank in advance, maxmaronna

gf777 commented 6 months ago

Hi To me it looks like you forgot the —recursive option when cloning the repo. There is a git command to fix that, or just start over Best Giulio

On Wed, Mar 20, 2024 at 8:42 PM maxmaronna @.***> wrote:

Hello, I am having issues to install gfastats in a new server:

(ngs) @.:~/01-SOFTWARE/gfastats/gfastats$ make -j g++ -g -std=gnu++14 -O3 -I./include -Igfalibs/include -Wall -Wextra -pthread -c src/main.cpp -o build/bin/.o/main g++ -g -std=gnu++14 -O3 -I./include -Igfalibs/include -Wall -Wextra -pthread -c src/input.cpp -o build/bin/.o/input make -j -C /home/maxmaronna/01-SOFTWARE/gfastats/gfastats/gfalibs CXXFLAGS="-g -std=gnu++14 -O3 -I./include -Igfalibs/include -Wall -Wextra " make[1]: Entering directory '/home/maxmaronna/01-SOFTWARE/gfastats/gfastats/gfalibs' make[1]: No targets specified and no makefile found. Stop. make[1]: Leaving directory '/home/maxmaronna/01-SOFTWARE/gfastats/gfastats/gfalibs' make: [Makefile:41: gfalibs] Error 2 make: Waiting for unfinished jobs.... src/input.cpp:8:10: fatal error: parallel-hashmap/phmap.h: No such file or directory

include <parallel-hashmap/phmap.h>

^~~~~~ compilation terminated. make: *** [Makefile:37: build/bin/.o/input] Error 1 In file included from src/main.cpp:7: ./include/main.h:31:10: fatal error: log.h: No such file or directory

include "log.h"

^~~ compilation terminated. make: *** [Makefile:37: build/bin/.o/main] Error 1

Thank in advance, maxmaronna

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maxmaronna commented 6 months ago

Hi Giulio, Thanks for your answer, I forgot the —recursive option. gfastats was installed properly (and it´s working great). Best maxmaronna

gf777 commented 6 months ago

nice! have fun