Configure error required bzlib h header file not found

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• Compiling dvdistaster: bzlib.h not found (dev files installed)

1. Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   Hey everyone… I was hoping to use the dvdisaster program to check a load of CDs and DVDs I have. When compiling, I get an error that bzlib.h is not found.

   Code:

   Looking for includes and libraries:
   Checking for bzlib.h: /usr/lib/ghc-7.0.3/haddock/bzlib-0.5.0.1 (user supplied, but seems not to work)
   bzlib.h not found.
   Please specify the include file location using the following option:
   --bz2-includes=DIR

   I have the development files and the debug files (just in case) and have ran apt-file search which returns:

   Code:

   libbz2-dev: /usr/include/bzlib.h
   libcomplearn1-headers: /usr/include/complearn-1.0/complearn/complearn-rcbzlib.h
   libghc-bzlib-doc: /usr/lib/ghc-7.0.3/haddock/bzlib-0.5.0.1/bzlib.haddock

   I’ve tried the following: (I’m not very good at CLI so I’m gonna post every command I’ve ran in case I’m making a mistake)
   ./compile—bz2-includes=/usr/include/bzlib.h
   ./compile—bz2-includes=/usr/include/
   ./compile—bz2-includes=/usr/include
   Those last two are just because I’m unsure whether it’s asking for the full path or the directory, and also I’m never sure whether putting a last slash will make a difference.
   Also, I’ve tried those above commands for the other two files that apt-file gave me, just in case they worked. Probably really silly but *shrug* I just wanna check my dvds

   Curiously, when I cd to usr/include ls doesn’t return any bzlib.h. I’m out of ideas. Anyone have any ideas?

   Paula

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2. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   Moved to Packaging and Compiling Programs.

   ---

3. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   I myself had a problem with that same library when compiling a different program. I can’t quite recall what worked to fix it (I tried a ton of different things). I think what I had to do (after basically installing every variant of libbz2 available in the repos!) was manually download and compile bzip2, and then reboot the system so that it was aware of the location of the new location of the library (not sure why this was necessary either, but the compiler kept saying that I didn’t have the files until I did this).

   So (and hopefully someone comes along with a less clunky, more elegant solution), you can try to install all of the libbz2 packages in the repos:

   Code:

   sudo apt-get install libbz2-1.0 libbz2-dev libbz2-ocaml libbz2-ocaml-dev

   If your prog still doesn’t compile, then try installing bzip2 manually from http://bzip.org/, reboot your system, and try compiling the DVD program again.

   Hope that works!

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4. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   Are you using the unstable (79) branch? As it can be exactly that… and is frequently feature missing

   The stable version is in the repos and relatively up to date — no compilation required

   Code:

   cd /fridge/beer | drink && fallover

   ---

5. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   Originally Posted by drmrgd
   

   I myself had a problem with that same library when compiling a different program. I can’t quite recall what worked to fix it (I tried a ton of different things). I think what I had to do (after basically installing every variant of libbz2 available in the repos!) was manually download and compile bzip2, and then reboot the system so that it was aware of the location of the new location of the library (not sure why this was necessary either, but the compiler kept saying that I didn’t have the files until I did this).

   So (and hopefully someone comes along with a less clunky, more elegant solution), you can try to install all of the libbz2 packages in the repos:

   Code:

   sudo apt-get install libbz2-1.0 libbz2-dev libbz2-ocaml libbz2-ocaml-dev

   If your prog still doesn’t compile, then try installing bzip2 manually from http://bzip.org/, reboot your system, and try compiling the DVD program again.

   Hope that works!

   Drmrgod — I have know idea how or why, but installing libbz2 worked. Now I can’t seem to figure out what I’d been searching synaptic for the other day…oh well, thanks for your reply, it gave me the right package to search for

   How does one become proficient at this type of thing…surely Google and Ubuntuforums aren’t the only way forward? I mean, how do you develop the Linux/Ubuntu logic? I’ve tried the documentation but it still seems beyond me.

   Thanks again!!

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6. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   Originally Posted by _Smiler_
   

   How does one become proficient at this type of thing…surely Google and Ubuntuforums aren’t the only way forward? I mean, how do you develop the Linux/Ubuntu logic?

   First of all, you’re asking about compiling programs. That’s not an easy task for most people, and it’s why most Ubuntu users rely on the repositories. I can count on one hand the number of applications I’ve built from source over the past year.

   Now if you want to build a personal version of a particular application that already exists in the repositories, then you can use the convenient «build-dep» option to apt-get. Suppose, for instance, you wanted to build a more up-to-date version of mplayer. You can run:

   Code:

   sudo apt-get build-dep mplayer

   and it should download and install all the required libraries and header files for you.

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7. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   You marked this thread [SOLVED], but you didn’t tell us what fixed the problem for you. Please elaborate so others can learn as well.

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8. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   Originally Posted by SeijiSensei
   

   You marked this thread [SOLVED], but you didn’t tell us what fixed the problem for you.

   I have removed the ‘Solved’ tag for the above reason.

   OP, please share your solution. The ‘Solved’ tag is for everyone’s benefit, not just yours.

   ---

9. Re: Compiling dvdistaster: bzlib.h not found (dev files installed)
   

   Am I missing something? The OP said

   I have know idea how or why, but installing libbz2 worked.

   (which happens to be the solution I was after…)

   cheers!

   ---

BiocManager::install("Rhtslib")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'Rhtslib'
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.9/bioc/src/contrib/Rhtslib_1.16.1.tar.gz'
Content type 'application/x-gzip' length 1470655 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/usr/local/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/RtmpKf9Lh3/R.INSTALL16fb856e1fa4b/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:130: warning: overriding recipe for target '.c.o'
/usr/local/lib/R/etc/Makeconf:167: warning: ignoring old recipe for target '.c.o'
gcc -g -Wall -O2 -fpic -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -fpic -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -fpic -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -fpic -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -fpic -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -fpic -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -fpic -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -fpic -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -fpic -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc -g -Wall -O2 -fpic -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -fpic -I.  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -fpic -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -fpic -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -fpic -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -fpic -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -fpic -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -fpic -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -fpic -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -fpic -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -fpic -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -fpic -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -fpic -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -fpic -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -fpic -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -fpic -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -fpic -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -fpic -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -fpic -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -fpic -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -fpic -I.  -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c:57:19: fatal error: bzlib.h: No such file or directory
 #include <bzlib.h>
                   ^
compilation terminated.
Makefile.Rhtslib:130: recipe for target 'cram/cram_io.o' failed
make[1]: Leaving directory '/tmp/RtmpKf9Lh3/R.INSTALL16fb856e1fa4b/Rhtslib/src/htslib-1.7'
make[1]: *** [cram/cram_io.o] Error 1
Makevars.common:23: recipe for target 'htslib' failed
make: *** [htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/rstudio/env/velocyto_R/packrat/lib/x86_64-pc-linux-gnu/3.6.1/Rhtslib’

Hit:1 http://security-cdn.debian.org/debian-security stretch/updates InRelease 
Ign:2 http://cdn-fastly.deb.debian.org/debian stretch InRelease 
Get:3 http://cdn-fastly.deb.debian.org/debian stretch-updates InRelease [91.0 kB] 
Hit:4 http://cdn-fastly.deb.debian.org/debian stretch Release 
Fetched 91.0 kB in 1s (59.9 kB/s) 
Reading package lists... Done 
Reading package lists... Done 
Building dependency tree        
Reading state information... Done 
Note, selecting 'zlib1g-dev' instead of 'libz-dev'
zlib1g-dev is already the newest version (1:1.2.8.dfsg-5).
0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.

─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.1 (2019-07-05)
 os       Debian GNU/Linux 9 (stretch)
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Etc/UTC                     
 date     2019-09-17                  

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.1)
 BiocManager   1.30.4  2018-11-13 [1] CRAN (R 3.6.1)
 cli           1.1.0   2019-03-19 [1] CRAN (R 3.6.1)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 3.6.1)
 packrat       0.5.0   2018-11-14 [1] CRAN (R 3.6.1)
 rstudioapi    0.10    2019-03-19 [1] CRAN (R 3.6.1)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.6.1)
 withr         2.1.2   2018-03-15 [1] CRAN (R 3.6.1)

[1] /home/rstudio/env/velocyto_R/packrat/lib/x86_64-pc-linux-gnu/3.6.1
[2] /home/rstudio/env/velocyto_R/packrat/lib-ext/x86_64-pc-linux-gnu/3.6.1
[3] /home/rstudio/env/velocyto_R/packrat/lib-R/x86_64-pc-linux-gnu/3.6.1