Ubuntu install: /usr/bin/ld: cannot find -ljpeg

snalbansed · Nov 17th 2016

Hi Marcel, all

On installing 1.4.19beta3 I get the following error after choosing my database type when running maklinux:

/usr/bin/ld: cannot find -ljpeg

This is on a fresh Ubuntu 16.04.1 server install.

Is there a library that I need to install first?

Thanks

Ed

marcelvanherk · Nov 17th 2016

Hi,

try to delete -ljpeg, jpeg-6c is the actual library. I will test that Ubuntu later.

Marcel

snalbansed · Nov 17th 2016

Should I just remove that argument from the maklinux script?

marcelvanherk · Nov 17th 2016

Yep,

Marcel

snalbansed · Nov 17th 2016

Thanks. I'll try that tomorrow.

marcelvanherk · Nov 17th 2016

I think the errors are mine, do not edit maklinux; Try this instead:

unzip all files to here
chmod 777 maklinux
chmod 777 src/dgate/jpeg-6c/configure
mkdir data/dbase
./maklinux

After this dgate works. The webserver not yet, unfortunately.
try this:

sudo rm /usr/lib/cgi-bin/dgate
sudo rm /usr/lib/cgi-bin/acrnema.map
sudo rm /usr/lib/cgi-bin/dgate.dic

sudo rm /usr/lib/cgi-bin/newweb/dgate
sudo rm /usr/lib/cgi-bin/newweb/acrnema.map
sudo rm /usr/lib/cgi-bin/newweb/dgate.dic

sudo cp dgate /usr/lib/cgi-bin
sudo cp dgate /usr/lib/cgi-bin/newweb
sudo cp dgate.dic /usr/lib/cgi-bin
sudo cp dgate.dic /usr/lib/cgi-bin/newweb
sudo cp acrnema.map /usr/lib/cgi-bin
sudo cp acrnema.map /usr/lib/cgi-bin/newweb

Sorry for the mixups!

Marcel

snalbansed · Nov 17th 2016

Thanks for trying it out!

I'll give the new instructions a try tomorrow.

marcelvanherk · Nov 17th 2016

Here is a fixed maklinux, please try this out:

Bash

#!/bin/bash
# mvh 20160425 for 1.4.19beta
# mvh 20160516 use ln -s for shared server/webserver configs
# mvh 20161117 back to cp, added chmod for src/dgate/jpeg-6c/configure 


#DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SRC=./src/dgate;
CONF=./linux/conf;
LINUX=./linux;


chmod 777 src/dgate/jpeg-6c/configure
cd src/dgate/jpeg-6c
./configure
make
sudo make install
cd ../../..


echo "Please choose DB type";


options=("mysql" "postgres" "sqlite" "dbase" "Quit")
select opt in "${options[@]}"
do
    case $opt in
        "mysql")
			gcc -o $SRC/lua.o -c $SRC/lua_5.1.5/all.c -I$SRC/lua_5.1.5 -DLUA_USE_DLOPEN -DLUA_USE_POSIX;
			g++ -std=c++11 -o $SRC/charls.o -c $SRC/charls/all.cpp -I$SRC/charls
			gcc -o $SRC/openjpeg.o -c $SRC/openjpeg/all.c -I$SRC/openjpeg
			g++ -std=c++11 -I/usr/local/mysql/include -I/usr/include/mysql -DUNIX -DNATIVE_ENDIAN=1 -DHAVE_LIBJPEG -DUSEMYSQL -DHAVE_LIBCHARLS -DHAVE_LIBOPENJPEG2 -Wno-write-strings $SRC/lua.o $SRC/charls.o $SRC/openjpeg.o -o dgate -lpthread -ldl -I$SRC/src $SRC/src/total.cpp -I$SRC/dicomlib -L/usr/local/mysql/lib -L/usr/lib/mysql -lmysqlclient -ljpeg -Ijpeg-6c -Ljpeg-6c -I$SRC/lua_5.1.5 -I$SRC/openjpeg -I$SRC/charls -Wno-multichar;
			break;
			;;
        "postgres")
			export LD_LIBRARY_PATH="/usr/include/postgresql/";
			gcc -o $SRC/lua.o -c $SRC/lua_5.1.5/all.c -I$SRC/lua_5.1.5 -DLUA_USE_DLOPEN -DLUA_USE_POSIX;
			g++ -std=c++11 -o $SRC/charls.o -c $SRC/charls/all.cpp -I$SRC/charls
			gcc -o $SRC/openjpeg.o -c $SRC/openjpeg/all.c -I$SRC/openjpeg
			g++ -std=c++11 -I/usr/include/postgresql/ -DUNIX -DNATIVE_ENDIAN=1 -DHAVE_LIBJPEG -DPOSTGRES -DHAVE_LIBCHARLS -DHAVE_LIBOPENJPEG2 -Wno-write-strings $SRC/lua.o $SRC/charls.o $SRC/openjpeg.o -o dgate -lpthread -ldl -I$SRC/src $SRC/src/total.cpp -I$SRC/dicomlib -L/usr/local/pgsql/lib -lpq  -ljpeg -I$SRC/jpeg-6c -L$SRC/jpeg-6c -I$SRC/lua_5.1.5 -I$SRC/openjpeg -I$SRC/charls -Wno-multichar;
			break;
			;;
        "sqlite")
			gcc -o $SRC/lua.o -c $SRC/lua_5.1.5/all.c -I$SRC/lua_5.1.5 -DLUA_USE_DLOPEN -DLUA_USE_POSIX;
			gcc -c -DTHREADSAFE=1 -DHAVE_USLEEP $SRC/sqlite3/sqlite3.c -I$SRC/sqlite3 -o $SRC/sqlite3.o;
			g++ -std=c++11 -o $SRC/charls.o -c $SRC/charls/all.cpp -I$SRC/charls
			gcc -o $SRC/openjpeg.o -c $SRC/openjpeg/all.c -I$SRC/openjpeg
			g++ -std=c++11 -DUNIX -DNATIVE_ENDIAN=1 -DHAVE_LIBJPEG -DUSESQLITE -DHAVE_LIBCHARLS -DHAVE_LIBOPENJPEG2 -Wno-write-strings $SRC/sqlite3.o $SRC/lua.o $SRC/charls.o $SRC/openjpeg.o -o dgate -lpthread -ldl -I$SRC/src $SRC/src/total.cpp -I$SRC/dicomlib -I$SRC/sqlite3 -ljpeg -I$SRC/jpeg-6c -L$SRC/jpeg-6c -I$SRC/lua_5.1.5 -I$SRC/openjpeg -I$SRC/charls -Wno-multichar;
			rm $SRC/sqlite3.o;
			break;
			;;
	"dbase")
			gcc -o $SRC/lua.o -c $SRC/lua_5.1.5/all.c -I$SRC/lua_5.1.5 -DLUA_USE_DLOPEN -DLUA_USE_POSIX;
			g++ -std=c++11 -o $SRC/charls.o -c $SRC/charls/all.cpp -I$SRC/charls
			gcc -o $SRC/openjpeg.o -c $SRC/openjpeg/all.c -I$SRC/openjpeg
			g++ -std=c++11 -DUNIX -DNATIVE_ENDIAN=1 -DHAVE_LIBJPEG -DHAVE_LIBCHARLS -DHAVE_LIBOPENJPEG2 -Wno-write-strings $SRC/lua.o $SRC/charls.o $SRC/openjpeg.o -o dgate -lpthread -ldl -I$SRC/src $SRC/src/total.cpp -I$SRC/dicomlib -ljpeg -I$SRC/jpeg-6c -L$SRC/jpeg-6c -I$SRC/lua_5.1.5 -I$SRC/openjpeg -I$SRC/charls -Wno-multichar;
			break;	
			;;
        "Quit")
            break
            ;;
        *) echo invalid option;;
    esac
done


if [ $opt != "Quit" ] 
then


	rm $SRC/lua.o;
	rm $SRC/charls.o;
	rm $SRC/openjpeg.o;


	pkill -9 dgate;
	sleep 0.2s;


	cp $CONF/dicom.ini.$opt dicom.ini;
	cp $CONF/dicom.sql.$opt dicom.sql;


	cp $LINUX/acrnema.map acrnema.map;
	cp $LINUX/dgatesop.lst dgatesop.lst;


	sudo cp ./dgate /usr/lib/cgi-bin/dgate ;
	sudo cp ./dgate /usr/lib/cgi-bin/newweb/dgate ;
	sudo cp ./dicom.sql /usr/lib/cgi-bin/dicom.sql ;
	sudo cp ./acrnema.map /usr/lib/cgi-bin/acrnema.map ;
	sudo cp ./acrnema.map /usr/lib/cgi-bin/newweb/acrnema.map ;


	sudo cp -r ./webserver/cgi-bin/* /usr/lib/cgi-bin;
	sudo cp -r ./webserver/cgi-bin/.lua /usr/lib/cgi-bin;
	sudo cp -r ./webserver/cgi-bin/.lua.linux /usr/lib/cgi-bin;
	sudo cp /usr/lib/cgi-bin/dicom.ini.linux /usr/lib/cgi-bin/dicom.ini;
	sudo cp /usr/lib/cgi-bin/newweb/dicom.ini.linux /usr/lib/cgi-bin/newweb/dicom.ini;
	sudo cp /usr/lib/cgi-bin/.lua.linux /usr/lib/cgi-bin/.lua;


	sudo cp -r ./webserver/htdocs/* /var/www;
	sudo cp -r ./webserver/htdocs/* /var/www/html;

	mkdir data/dbase
fi

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However, you need to delete the incorrect cgi-bin hardlinks as per the previous post

snalbansed · Nov 17th 2016

Thanks. Will do.

snalbansed · Nov 18th 2016

Hi Marcel

I'm wondering if the version I downloaded was the latest? The reason I'm asking is that the maklinux I have a/ didn't have the # mvh 20160516 comment line and b/ maklinux is within src/dgate whereas your code assumes that maklinux is at the top...

Having moved (the new) maklinux to the top, and having installed build-essential (not in your instructions - make is needed), I now get the following error before the DB choice:

Code

/usr/bin/install -c -m 644 ./cjpeg.1 /usr/local/man/man1/cjpeg.1
/usr/bin/install: cannot create regular file '/usr/local/man/man1/cjpeg.1': No such file or directory
Makefile:200: recipe for target 'install' failed
make: *** [install] Error 1

Any ideas?

Thanks

Ed

snalbansed · Nov 18th 2016

It was just that the man1 folder didn't exist in man.

marcelvanherk · Nov 18th 2016

Indeed, I got the same message and ignored it.

The make at the top level is the right one. I should delete the one in dgate.

Marcel

snalbansed · Nov 18th 2016

I see, I hadn't noticed that I'd copied over that one as the instructions had led me to the dgate folder.

Should dgate be linked into /usr/bin or something at some point so it is available generally, or is the idea to always run it from the folder it was extracted to?

marcelvanherk · Nov 18th 2016

Hi,

dgate is run from the following folders

root of zip file - as server

/usr/lib/cgi-bin - as old web interface
/usr/lib/newweb - as new web interface

to be able to run, it also needs a dicom.ini, dicom.dic and (for server) acrnema.map and dicom.sql.

These files could be hardlinked to the root of the zip folder, but my attemp at doing so was flawed.

So I would not link the server's dgate as it assumes relative position of the other files.

Marcel

snalbansed · Nov 18th 2016

Do you not mean

/usr/lib/cgi-bin - as old web interface
/usr/lib/cgi-bin/newweb - as new web interface

?

marcelvanherk · Nov 18th 2016

Yep,

should not do this be heart ...

Marcel

snalbansed · Nov 18th 2016

My final setup notes, in case it is of use for editing the linux instructions. This is on a fresh Ubuntu 16.04.1 server installed as a LXD container:

Code

sudo apt install build-essential apache2 libpq-dev postgresql unzipsudo a2enmod cgidsudo service apache2 restart

Copied download of dicomserver1419beta3b.zip

Code

mkdir conquestcd conquestunzip ../dicomserver1419beta3b.zip

We need a new version of maklinux from Marcel van Herk http://forum.image-systems.biz…eply&f=33&t=45654#pr59441

Code

mv maklinux{,.original}nano maklinux

Paste in new version copied from forum

Code

chmod 777 maklinuxchmod 777 src/dgate/jpeg-6c/configuresudo mkdir /usr/local/man/man1./maklinux

Chose option 3) sqlite for now, just to get started
For some reason, the script complained that

Code

cp: cannot create regular file '/usr/lib/cgi-bin/newweb/dgate': No such file or directorycp: cannot create regular file '/usr/lib/cgi-bin/newweb/acrnema.map': No such file or directory

despite the fact that it did exist. Ran it a second time and this time the only complaint was regarding the directory data/dbase already existing.

Copied dicom.sql and dgatesop.lst into /usr/lib/cgi-bin/newweb/ as they are both missing. It works without dgatesop.lst, but doesn't have the newer SOP Class UIDs such as BTO

Code

mkdir /mnt/archive/datachmod 777 /mnt/archive/data

Edited dicom.ini, partly to add specific paths, partly because the version in /usr/lib/cgi-bin/newweb is relatively brief!: sudo nano /usr/lib/cgi-bin/newweb/dicom.ini

Code

#mvh 20151206  1.4.17d compatibility#mvh 20160314  for 1.4.19beta[sscscp]MicroPACS                = sscscpACRNemaMap               = acrnema.mapDictionary               = dgate.dicWebServerFor             = 127.0.0.1MyACRNema                = MYAETTCPPort                  = 104SOPClassList             = dgatesop.lstSQLServer                = /path/to/conquest/data/dbase/conquest.db3SQLite                   = 1# Configure serverImportExportDragAndDrop  = 1ZipTime                  = 05:UIDPrefix                = 99999.99999EnableComputedFields     = 1# Configuration of compression for incoming images and archivalDroppedFileCompression   = unIncomingCompression      = unArchiveCompression       = as# For debug informationPACSName                 = CONQUESTSRV1OperatorConsole          = 127.0.0.1DebugLevel               = 0# Configuration of disk(s) to store imagesMAGDeviceFullThreshold   = 30MAGDevices               = 1MAGDevice0               = /path/to/data/[webdefaults]size     = 560dsize    = 0compress = j2iconsize = 84graphic  = jpgviewer   = wadoseriesviewerstudyviewer = wadostudyviewer[DefaultPage]source = *.lua[AnyPage]source = start.luaexceptions=start,listpatients,liststudies,listseries,listimageswiththumbs,listimages,wadostudyviewer,wadoseriesviewer,wadoviewerhelp,slice,listtrials,listtrialpatients

Edited acrnema.map to match MyACRNema setting.

Finally:

Code

sudo /usr/lib/cgi-bin/newweb/dgate -v -r 
sudo /usr/lib/cgi-bin/newweb/dgate -v

marcelvanherk · Nov 18th 2016

Thanks!

Marcel

Ubuntu install: /usr/bin/ld: cannot find -ljpeg

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