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glencoesoftware / bioformats2raw

Bio-Formats image file format to raw format converter
GNU General Public License v2.0
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The input line is too long. The syntax of the command is incorrect. #14

Closed camlloyd closed 1 year ago

camlloyd commented 4 years ago

Trying to run bioformats2raw on Windows 10 produces the following error:

The input line is too long.
The syntax of the command is incorrect.

Without digging into Gradle, a workaround is to change the long CLASSPATH variable after building the bioformats2raw.bat file from:

set CLASSPATH=%APP_HOME%\lib\bioformats2raw-0.2.0-SNAPSHOT.jar;%APP_HOME%\lib\formats-gpl-6.2.1.jar;%APP_HOME%\lib\picocli-3.9.6.jar;%APP_HOME%\lib\n5-blosc-1.0.0.jar;%APP_HOME%\lib\n5-2.1.2.jar;%APP_HOME%\lib\formats-bsd-6.2.1.jar;%APP_HOME%\lib\formats-api-6.2.1.jar;%APP_HOME%\lib\ome-xml-6.0.1.jar;%APP_HOME%\lib\metakit-5.3.2.jar;%APP_HOME%\lib\ome-poi-5.3.3.jar;%APP_HOME%\lib\ome-codecs-0.2.5.jar;%APP_HOME%\lib\ome-common-6.0.3.jar;%APP_HOME%\lib\ome-mdbtools-5.3.2.jar;%APP_HOME%\lib\jxrlib-all-0.2.1.jar;%APP_HOME%\lib\cdm-4.6.13.jar;%APP_HOME%\lib\logback-classic-1.1.1.jar;%APP_HOME%\lib\native-lib-loader-2.1.4.jar;%APP_HOME%\lib\httpservices-4.6.13.jar;%APP_HOME%\lib\slf4j-api-1.7.22.jar;%APP_HOME%\lib\JWlz-1.4.0.jar;%APP_HOME%\lib\minio-5.0.2.jar;%APP_HOME%\lib\joda-time-2.8.1.jar;%APP_HOME%\lib\kryo-2.24.0.jar;%APP_HOME%\lib\jhdf5-14.12.6.jar;%APP_HOME%\lib\json-20090211.jar;%APP_HOME%\lib\xz-1.8.jar;%APP_HOME%\lib\lz4-java-1.5.0.jar;%APP_HOME%\lib\gson-2.8.5.jar;%APP_HOME%\lib\scijava-common-2.77.0.jar;%APP_HOME%\lib\commons-compress-1.18.jar;%APP_HOME%\lib\jblosc-1.0.1.jar;%APP_HOME%\lib\commons-io-2.6.jar;%APP_HOME%\lib\guava-27.1-jre.jar;%APP_HOME%\lib\logback-core-1.1.1.jar;%APP_HOME%\lib\xalan-2.7.2.jar;%APP_HOME%\lib\serializer-2.7.2.jar;%APP_HOME%\lib\specification-6.0.1.jar;%APP_HOME%\lib\turbojpeg-6.2.1.jar;%APP_HOME%\lib\jgoodies-forms-1.7.2.jar;%APP_HOME%\lib\perf4j-0.9.16.jar;%APP_HOME%\lib\metadata-extractor-2.11.0.jar;%APP_HOME%\lib\xercesImpl-2.8.1.jar;%APP_HOME%\lib\httpmime-4.5.1.jar;%APP_HOME%\lib\google-http-client-xml-1.20.0.jar;%APP_HOME%\lib\google-http-client-1.20.0.jar;%APP_HOME%\lib\httpclient-4.5.1.jar;%APP_HOME%\lib\commons-logging-1.2.jar;%APP_HOME%\lib\c3p0-0.9.5.3.jar;%APP_HOME%\lib\jackson-databind-2.9.8.jar;%APP_HOME%\lib\jackson-core-2.9.8.jar;%APP_HOME%\lib\jackson-annotations-2.9.8.jar;%APP_HOME%\lib\minlog-1.2.jar;%APP_HOME%\lib\objenesis-2.1.jar;%APP_HOME%\lib\commons-lang-2.4.jar;%APP_HOME%\lib\parsington-1.0.3.jar;%APP_HOME%\lib\eventbus-1.4.jar;%APP_HOME%\lib\junit-4.12.jar;%APP_HOME%\lib\jna-4.2.2.jar;%APP_HOME%\lib\okhttp-3.7.0.jar;%APP_HOME%\lib\okio-1.12.0.jar;%APP_HOME%\lib\failureaccess-1.0.1.jar;%APP_HOME%\lib\listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar;%APP_HOME%\lib\jsr305-3.0.2.jar;%APP_HOME%\lib\checker-qual-2.5.2.jar;%APP_HOME%\lib\error_prone_annotations-2.2.0.jar;%APP_HOME%\lib\j2objc-annotations-1.1.jar;%APP_HOME%\lib\animal-sniffer-annotations-1.17.jar;%APP_HOME%\lib\xml-apis-1.3.04.jar;%APP_HOME%\lib\ome-jai-0.1.0.jar;%APP_HOME%\lib\jgoodies-common-1.7.0.jar;%APP_HOME%\lib\xmpcore-5.1.3.jar;%APP_HOME%\lib\mchange-commons-java-0.2.15.jar;%APP_HOME%\lib\hamcrest-core-1.3.jar;%APP_HOME%\lib\xpp3-1.1.4c.jar;%APP_HOME%\lib\commons-codec-1.9.jar;%APP_HOME%\lib\httpcore-4.4.3.jar

to a wildcard, since it exceeds the limit of 2047 characters for Windows NT(?):

set CLASSPATH=%APP_HOME%\lib\*
melissalinkert commented 4 years ago

Thanks for reporting this, @camlloyd. The CLASSPATH length does seem to be a known issue with Gradle, see https://github.com/gradle/gradle/issues/1989.

The length of the APP_HOME folder name is important. I couldn't immediately reproduce the issue when running .\bin\bioformats2raw.bat from a folder with a 70 character name. Switching to a folder with an 82 character name results in the The input line is too long error.

If renaming/shortening the path name is an option, that's probably the easier immediate work-around since it won't require changing bioformats2raw.bat after every build.

camlloyd commented 4 years ago

Thanks @melissalinkert!

jburel commented 1 year ago

See https://github.com/ome/conda-raw2ometiff/pull/9 for conda (similar for bioformats2raw)

sbesson commented 1 year ago

From a quick search, it looks like a workaround currently used elsewhere is to patch these lines within the startScripts section of the Gradle build script https://github.com/search?q=CLASSPATH+winFileText&type=code

Possibly something worth trying out for an upcoming bioformats2raw/raw2ometiff release