Missing dependencies after successful installation

[AnzhelikaVetMedUni]

Hey!

I have been trying to get GUAVA working for ATAC-seq analysis. I have installed GUAVA according to the manual and everything seems to have gone successfully:

I_NSTALLING GUAVA-1 dependencies

Operating system :Mac R is already installed ! R is already installed ! Installing R packages > >> > [1] ">>> >> > Loading BIOCONDUCTOR > >> >>>" Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). [1] ">>> >> > checking required packages > >> >>>" [1] ">>>>> Found: ggplot2 <<<<<" [1] ">>>>> Found: GenomicFeatures <<<<<" [1] ">>>>> Found: TxDb.Hsapiens.UCSC.hg19.knownGene <<<<<" [1] ">>>>> Found: TxDb.Mmusculus.UCSC.mm10.knownGene <<<<<" [1] ">>>>> Found: org.Hs.eg.db <<<<<" [1] ">>>>> Found: org.Mm.eg.db <<<<<" [1] ">>>>> Found: ChIPpeakAnno <<<<<" [1] ">>>>> Found: GO.db <<<<<" [1] ">>>>> Found: KEGG.db <<<<<" [1] ">>>>> Found: Rsubread <<<<<" [1] ">>>>> Found: DESeq2 <<<<<"

CONDA is already installed !

---------- Adding BIOCONDA and other channels ---------------- Warning: 'r' already in 'channels' list, moving to the top Warning: 'defaults' already in 'channels' list, moving to the top Warning: 'conda-forge' already in 'channels' list, moving to the top Warning: 'bioconda' already in 'channels' list, moving to the top

Installing dependencies > >> >>>

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

FOUND: java <<<<< FOUND: bedtools <<<<< FOUND: bowtie <<<<< FOUND: bowtie2 <<<<< FOUND: cutadapt <<<<< FOUND: fastqc <<<<< FOUND: samtools <<<<< FOUND: picard <<<<< FOUND: igv <<<<< FOUND: bedGraphToBigWig <<<<<

MACS2 is already installed !

Finished <<<<<<<<<_

But when I try to run the ATAC-seq data analysis MACS2 seems to be missing:

GUAVA version 1 _Operating System of machine :Mac OS X cutadapt: Working! bowtie: Working! bowtie2: Working! fastqc: Working! samtools: Working! MACS2 version (macs2 2.1.1.20160309) : NOT FOUND !!! Picard: Working! bedtools: Working! bedGraphToBigWig: Working! igv: Working!

There are missing dependancies! Please use configure.sh to install dependencies. If you are having difficulties in installing dependencies, please report issue at GitHub.

https://github.com/MayurDivate/GUAVASourceCode/issues EXIT(GUAVA) ..._

So I am not quite sure what to do. Could you possibly help?

Thank you!

Anzhelika

[syed1789]

I also having the same problem..

[MayurDivate]

Hello everyone,

Sorry for the late reply.

Recently MACS2 got updated from 2.1.1.20160309 to 2.1.1 version. As GUAVA automatically installs the latest MACS2 version you get the above error.

Please use the command below to install correct MACS2 version. pip install MACS2==2.1.1.20160309 (use sudo if required)

We will fix this issue in the upcoming release.

Cheers, Mayur

[syed1789]

thanks

On Wed, Nov 14, 2018 at 1:42 AM Mayur Divate notifications@github.com wrote:

Hello everyone,

Sorry for the late reply.

Recently MACS2 got updated from 2.1.1.20160309 to 2.1.1 version. As GUAVA automatically installs the latest MACS2 version you get the above error.

Please use the command below to install correct MACS2 version. pip install MACS2==2.1.1.20160309 (use sudo if required)

We will fix this issue in the upcoming release.

Cheers, Mayur

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/MayurDivate/GUAVASourceCode/issues/3#issuecomment-438342315, or mute the thread https://github.com/notifications/unsubscribe-auth/AWG1Ew02apKQFaEPBsP9W6r6yYZ0zM1qks5uuvZagaJpZM4X6opu .

[jrainger3]

I am having the same problem, but when I run.. pip install MACS2==2.1.1.20160309 it says Complete output from command python setup.py egg_info: CRITICAL:Numpy must be installed!

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/vv/yh9n7lws3gs_xn322srw52dnggt16m/T/pip-install-jvDqP5/MACS2/

Please help. Thanks!

[jrainger3]

I fixed it using this: $ python -m pip install --user numpy scipy matplotlib ipython jupyter pandas sympy nose $ pip install MACS2==2.1.1.20160309 $ sh ./configure.sh All good!

[woeulii]

Hi, I am new to GUAVA and also get the problem with MACS2. I tried all of the suggestions above but still get this error:

(base) tsf-484-wpa-5-096:~ wohlwend$ pip install MACS2==2.1.1.20160309 Collecting MACS2==2.1.1.20160309 Using cached https://files.pythonhosted.org/packages/9f/99/a8ac96b357f6b0a6f559fe0f5a81bcae12b98579551620ce07c5183aee2c/MACS2-2.1.1.20160309.tar.gz Requirement already satisfied: numpy>=1.6 in ./miniconda2/lib/python2.7/site-packages (from MACS2==2.1.1.20160309) (1.16.2) Building wheels for collected packages: MACS2 Running setup.py bdist_wheel for MACS2 ... error Complete output from command /Users/wohlwend/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/v2/08jgbwrd35d3qvt23279xrmw0000gn/T/pip-install-3MxBPE/MACS2/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /private/var/folders/v2/08jgbwrd35d3qvt23279xrmw0000gn/T/pip-wheel-6Hpc6q --python-tag cp27: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.6-x86_64-2.7 creating build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/OutputWriter.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/refinepeak_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/cmbreps_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/pileup_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgcmp_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/Constants.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgdiff_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/predictd_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/filterdup_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgopt_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/init.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/OptValidator.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/callpeak_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgbroadcall_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgpeakcall_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/randsample_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/diffpeak_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 creating build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/test_processing.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/test_threading.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/init.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/BinKeeper.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO running build_ext building 'MACS2.Prob' extension creating build/temp.macosx-10.6-x86_64-2.7 creating build/temp.macosx-10.6-x86_64-2.7/MACS2 gcc -fno-strict-aliasing -I/Users/wohlwend/miniconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/wohlwend/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/wohlwend/miniconda2/include/python2.7 -c MACS2/Prob.c -o build/temp.macosx-10.6-x86_64-2.7/MACS2/Prob.o -w -O3 -ffast-math xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command 'gcc' failed with exit status 1

---

Failed building wheel for MACS2 Running setup.py clean for MACS2 Failed to build MACS2 Installing collected packages: MACS2 Running setup.py install for MACS2 ... error Complete output from command /Users/wohlwend/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/v2/08jgbwrd35d3qvt23279xrmw0000gn/T/pip-install-3MxBPE/MACS2/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/v2/08jgbwrd35d3qvt23279xrmw0000gn/T/pip-record-Z50iQb/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.macosx-10.6-x86_64-2.7 creating build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/OutputWriter.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/refinepeak_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/cmbreps_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/pileup_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgcmp_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/Constants.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgdiff_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/predictd_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/filterdup_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgopt_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/init.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/OptValidator.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/callpeak_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgbroadcall_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/bdgpeakcall_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/randsample_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 copying MACS2/diffpeak_cmd.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2 creating build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/test_processing.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/test_threading.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/init.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO copying MACS2/IO/BinKeeper.py -> build/lib.macosx-10.6-x86_64-2.7/MACS2/IO running build_ext building 'MACS2.Prob' extension creating build/temp.macosx-10.6-x86_64-2.7 creating build/temp.macosx-10.6-x86_64-2.7/MACS2 gcc -fno-strict-aliasing -I/Users/wohlwend/miniconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/wohlwend/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/wohlwend/miniconda2/include/python2.7 -c MACS2/Prob.c -o build/temp.macosx-10.6-x86_64-2.7/MACS2/Prob.o -w -O3 -ffast-math xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/Users/wohlwend/miniconda2/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/v2/08jgbwrd35d3qvt23279xrmw0000gn/T/pip-install-3MxBPE/MACS2/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /private/var/folders/v2/08jgbwrd35d3qvt23279xrmw0000gn/T/pip-record-Z50iQb/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/v2/08jgbwrd35d3qvt23279xrmw0000gn/T/pip-install-3MxBPE/MACS2/

Any help is greatly appreciated! Thanks in advance!

[roshsin]

Hello again,

I resolved miniconda loading issue. But, I am now running into MAC2S installation errors even though I have tried using different versions of Python (2.7, 3.6, 3.7). Additionally, I am observing dyld: Library not loaded. I tried all the suggestions mentioned here but it didn't work. Kindly advise on how I can overcome these!

Attached below are the errors I am running into right now:

INSTALLING GUAVA-1 dependencies

Operating system :Mac R is already installed ! R is already installed ! Installing R packages > >> > dyld: Library not loaded: @rpath/libreadline.6.2.dylib Referenced from: /Users/roshanisinha/miniconda3/envs/mywork2/lib/R/lib/libR.dylib Reason: image not found ./configure.sh: line 96: 26743 Abort trap: 6 Rscript ./lib/InstallRequiredPackages.R

CONDA is already installed !

---------- Adding BIOCONDA and other channels ---------------- Warning: 'r' already in 'channels' list, moving to the top Warning: 'defaults' already in 'channels' list, moving to the top Warning: 'conda-forge' already in 'channels' list, moving to the top Warning: 'bioconda' already in 'channels' list, moving to the top

Installing dependencies > >> >>>

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

FOUND: java <<<<< FOUND: bedtools <<<<< FOUND: bowtie <<<<< FOUND: bowtie2 <<<<< FOUND: cutadapt <<<<< FOUND: fastqc <<<<< FOUND: samtools <<<<< FOUND: picard <<<<< FOUND: igv <<<<< FOUND: bedGraphToBigWig <<<<<

Installing Numpy > >> >>> DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Requirement already satisfied: numpy in /Users/roshanisinha/miniconda3/envs/mywork2/lib/python2.7/site-packages (1.16.6)

Installing MACS2 > >> >>> DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Collecting macs2 Using cached MACS2-2.2.6.tar.gz (2.0 MB) ERROR: Command errored out with exit status 1: command: /Users/roshanisinha/miniconda3/envs/mywork2/bin/python2.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-esZVEH/macs2/setup.py'"'"'; file='"'"'/private/tmp/pip-install-esZVEH/macs2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /private/tmp/pip-pip-egg-info-B143Qx cwd: /private/tmp/pip-install-esZVEH/macs2/ Complete output (1 lines): CRITICAL: Python version must >= 3.6!

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Finished <<<<<<<<<

Thank you!

Rosh