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A robust, extensible metagenomics pipeline
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Installation error #223

Closed louiejtaylor closed 5 years ago

louiejtaylor commented 5 years ago

This issue is to address a problem with installation reported by @carolynePearl in two other threads:

The crux of the issue seems to be some sort of conda dependency issue with libgcc (quoted comment from carolynePearl):

2019-08-28 15:37:03 UTC [ info] Conda path: /home/Pearl/miniconda3 2019-08-28 15:37:03 UTC [ info] Sunbeam src: /home/Pearl/sunbeam-stable 2019-08-28 15:37:03 UTC [ info] Sunbeam env: 'sunbeam' 2019-08-28 15:37:05 UTC [ info] Conda already installed. 2019-08-28 15:37:05 UTC [ info] Creating Sunbeam environment... UnsatisfiableError: The following specifications were found to be incompatible with each other: Package libgcc conflicts for: jellyfish==1.1.11=1 -> libgcc bwa[version='>=0.7.17'] -> libgcc rust-bio-tools -> libgcc megahit[version='<1.2'] -> libgcc blast -> libgcc pysam -> libgcc minimap2 -> libgcc ....and many more pckages and ends with this: 2019-08-28 15:37:48 UTC [ error] Error in /home/Pearl/sunbeam-stable/install.sh in function debug_capture on line 50 2019-08-28 15:37:49 UTC [ error] Environment creation failed! 2019-08-28 15:37:49 UTC [ error] Try re-running with -v or -d, or file an issue on Github.

I have a few questions that might shed some light on the situation, but I've really never seen anything like this before. Here are a few questions that might help us figure out what's going on:

Finally, could you paste the full package list that conda complained about during the sunbeam install? I'm curious as to whether at some point way down on the list there are requirements for conflicting versions of libgcc.

Thank you!

Leaving this here for when I have more time to dig into this later--these issues (1,2) are potentially related and seem to suggest a particular version of conda is responsible (on an extremely cursory read).

carolynePearl commented 5 years ago
  1. i am working with Ubuntu 17.10 (GNU/Linux 4.13.0-46-generic x86_64)
  2. Yes i had installed miniconda2, however, i uninstalled it and installed Miniconda3
  3. conda 4.7.11

Here is the full package list: Pearl@ibr-svr-03:~/sunbeam-stable$ ./install.sh 2019-08-28 17:58:21 UTC [ info] Starting Sunbeam installation... 2019-08-28 17:58:21 UTC [ info] Conda path: /home/Pearl/miniconda3 2019-08-28 17:58:21 UTC [ info] Sunbeam src: /home/Pearl/sunbeam-stable 2019-08-28 17:58:21 UTC [ info] Sunbeam env: 'sunbeam' 2019-08-28 17:58:22 UTC [ info] Conda already installed. 2019-08-28 17:58:22 UTC [ info] Creating Sunbeam environment...

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package gmp conflicts for: blast -> gmp[version='>=6.1.2,<7.0a0'] Package python conflicts for: kraken-biom -> python[version='2.7.|3.4.|3.5.|3.6.'] grabseqs=0.3.4 -> python[version='>=3.6,<3.7.0a0'] cutadapt -> python[version='2.7.|3.4.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0'] biopython -> python[version='2.7.|3.4.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0'] pandas -> python[version='2.7.|3.4.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0'] pysam -> python[version='2.7.|3.4.|3.5.|3.6.|<3.0.0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0'] megahit[version='<1.2'] -> python[version='2.7.|3.4.|3.5.|3.6.'] ruamel.yaml -> python[version='2.7.|3.4.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0'] setuptools_scm -> python[version='2.7.|3.4.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0'] semantic_version -> python Package zlib conflicts for: minimap2 -> zlib[version='1.2.11.|1.2.8.|>=1.2.11,<1.3.0a0'] pysam -> zlib[version='1.2.11.|1.2.8.|>=1.2.11,<1.3.0a0'] rust-bio-tools -> zlib[version='1.2.11.|1.2.8.|>=1.2.11,<1.3.0a0'] bwa[version='>=0.7.17'] -> zlib[version='1.2.11.|1.2.8.|>=1.2.11,<1.3.0a0'] megahit[version='<1.2'] -> zlib[version='1.2.11.|1.2.8'] blast -> zlib[version='1.2.11.|1.2.8.|>=1.2.11,<1.3.0a0'] vsearch -> zlib[version='1.2.11.|1.2.8.|>=1.2.11,<1.3.0a0'] Package bcftools conflicts for: pysam -> bcftools[version='1.3.1|1.3|1.5.|1.6.|1.7.|1.9.|1.6|>=1.3|>=1.3,<1.4|>=1.4,<1.5|>=1.4.1|>=1.4.1,<1.5'] Package libgcc conflicts for: bwa[version='>=0.7.17'] -> libgcc jellyfish==1.1.11=1 -> libgcc vsearch -> libgcc minimap2 -> libgcc blast -> libgcc pysam -> libgcc kraken=1.0 -> libgcc megahit[version='<1.2'] -> libgcc rust-bio-tools -> libgcc Package networkx conflicts for: snakemake=5.5.0 -> networkx[version='>=2.0'] Package mmtf-python conflicts for: biopython -> mmtf-python Package openblas conflicts for: rust-bio-tools -> openblas[version='>=0.3.3,<0.3.4.0a0'] Package pytz conflicts for: pandas -> pytz[version='>=2017.2'] Package perl conflicts for: blast -> perl[version='5.22.0.|>=5.26.2,<5.26.3.0a0'] fastqc -> perl=5.22.0 bwa[version='>=0.7.17'] -> perl=5.22.0 kraken=1.0 -> perl=5.22.0 Package java-jdk conflicts for: trimmomatic=0.36 -> java-jdk fastqc -> java-jdk Package font-ttf-dejavu-sans-mono conflicts for: fastqc -> font-ttf-dejavu-sans-mono Package libstdcxx-ng conflicts for: vsearch -> libstdcxx-ng[version='>=4.9|>=7.3.0'] rust-bio-tools -> libstdcxx-ng[version='>=4.9|>=7.3.0'] pandas -> libstdcxx-ng[version='>=4.9|>=7.3.0'] blast -> libstdcxx-ng[version='>=4.9|>=7.3.0'] Package ruamel.yaml.clib conflicts for: ruamel.yaml -> ruamel.yaml.clib[version='>=0.1.2'] Package libgcc-ng conflicts for: cutadapt -> libgcc-ng[version='>=7.3.0'] blast -> libgcc-ng[version='>=4.9|>=7.3.0'] rust-bio-tools -> libgcc-ng[version='>=4.9|>=7.3.0'] vsearch -> libgcc-ng[version='>=4.9|>=7.3.0'] ruamel.yaml -> libgcc-ng[version='>=4.9|>=7.3.0'] pysam -> libgcc-ng[version='>=4.9|>=7.3.0'] minimap2 -> libgcc-ng[version='>=4.9|>=7.3.0'] bwa[version='>=0.7.17'] -> libgcc-ng[version='>=4.9|>=7.3.0'] pandas -> libgcc-ng[version='>=4.9|>=7.3.0'] biopython -> libgcc-ng[version='>=4.9|>=7.3.0'] Package setuptools conflicts for: ruamel.yaml -> setuptools setuptools_scm -> setuptools Package reportlab conflicts for: biopython -> reportlab Package aioeasywebdav conflicts for: snakemake=5.5.0 -> aioeasywebdav Package python-dateutil conflicts for: pandas -> python-dateutil[version='>=2.5.|>=2.6.1'] Package pcre conflicts for: blast -> pcre[version='>=8.41,<9.0a0'] Package boto3 conflicts for: snakemake=5.5.0 -> boto3 Package ftputil conflicts for: snakemake=5.5.0 -> ftputil[version='>=3.2'] Package perl-json conflicts for: blast -> perl-json Package python-irodsclient conflicts for: snakemake=5.5.0 -> python-irodsclient Package curl conflicts for: pysam -> curl[version='>=7.59.0,<8.0a0|>=7.64.0,<8.0a0|>=7.64.1,<8.0a0'] blast -> curl[version='>=7.64.1,<8.0a0'] Package pigz conflicts for: grabseqs=0.3.4 -> pigz cutadapt -> pigz Package openjdk conflicts for: trimmomatic=0.36 -> openjdk fastqc -> openjdk[version='>8.0.121|>=8.0.122|>=8.0.144'] Package nettle conflicts for: blast -> nettle[version='3.3|3.3.|>=3.3,<3.4.0a0|>=3.4.1,<3.5.0a0'] Package pandas conflicts for: snakemake=5.5.0 -> pandas Package entrez-direct conflicts for: blast -> entrez-direct Package jsonschema conflicts for: snakemake=5.5.0 -> jsonschema Package samtools conflicts for: pysam -> samtools[version='1.3.1|1.3|1.5.|1.6.|1.7.|1.9.|1.7|>=1.3|>=1.3,<1.4|>=1.4,<1.5|>=1.4.1|>=1.4.1,<1.5'] Package bzip2 conflicts for: blast -> bzip2[version='1.0.|>=1.0.6,<2.0a0'] vsearch -> bzip2[version='1.0.|>=1.0.6,<2.0a0'] pysam -> bzip2[version='>=1.0.8,<2.0a0'] Package perl-list-moreutils conflicts for: blast -> perl-list-moreutils Package starcode conflicts for: rust-bio-tools -> starcode Package wget conflicts for: grabseqs=0.3.4 -> wget Package boost conflicts for: blast -> boost[version='1.60.|1.61.|1.64.|>=1.66.0,<1.66.1.0a0|>=1.67.0,<1.67.1.0a0|>=1.68.0,<1.68.1.0a0'] Package argparse conflicts for: grabseqs=0.3.4 -> argparse Package snakemake-minimal conflicts for: snakemake=5.5.0 -> snakemake-minimal=5.5.0 Package gnutls conflicts for: blast -> gnutls[version='>=3.5.19,<3.6.0a0|>=3.6.5,<3.7.0a0'] Package ruamel conflicts for: ruamel.yaml -> ruamel Package sra-tools conflicts for: grabseqs=0.3.4 -> sra-tools[version='>2.9'] Package xz conflicts for: pysam -> xz[version='>=5.2.4,<5.3.0a0'] Package numpy conflicts for: pandas -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.|>=1.12.1,<2.0a0|>=1.14.6,<2.0a0|>=1.7|>=1.8|>=1.9|>=1.9.|>=1.9.3,<2.0a0'] biopython -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.8'] Package libdeflate conflicts for: pysam -> libdeflate[version='>=1.0,<1.1.0a0'] Package biom-format conflicts for: kraken-biom -> biom-format[version='>=2.1.5'] Package ruamel.ordereddict conflicts for: ruamel.yaml -> ruamel.ordereddict Package pysftp conflicts for: snakemake=5.5.0 -> pysftp[version='>=0.2.8'] Package xopen conflicts for: cutadapt -> xopen[version='>=0.1.1|>=0.3.2|>=0.5.0'] Package jinja2 conflicts for: snakemake=5.5.0 -> jinja2 Package gsl conflicts for: rust-bio-tools -> gsl[version='>=2.4,<2.5.0a0'] Package htslib conflicts for: pysam -> htslib[version='1.3.1|1.3|1.5.|1.6.|1.7.|1.7|>=1.3|>=1.3,<1.4|>=1.3.1,<1.4.0a0|>=1.3.2,<1.4.0a0|>=1.4,<1.5|>=1.4.1|>=1.4.1,<1.5|>=1.7,<1.8.0a0|>=1.9,<1.10.0a0'] Package pygraphviz conflicts for: snakemake=5.5.0 -> pygraphviz Package fontconfig conflicts for: fastqc -> fontconfig Package jellyfish conflicts for: kraken=1.0 -> jellyfish=1 Package requests conflicts for: grabseqs=0.3.4 -> requests Package dnaio conflicts for: cutadapt -> dnaio[version='>=0.3'] Package psutil conflicts for: snakemake=5.5.0 -> psutil Package perl-archive-tar conflicts for: blast -> perl-archive-tar Package google-cloud-storage conflicts for: snakemake=5.5.0 -> google-cloud-storage Package dropbox conflicts for: snakemake=5.5.0 -> dropbox[version='>=7.2.1'] Package filechunkio conflicts for: snakemake=5.5.0 -> filechunkio[version='>=1.6'] Package perl-threaded conflicts for: fastqc -> perl-threaded Package typing conflicts for: ruamel.yaml -> typing

2019-08-28 17:58:46 UTC [ error] Error in /home/Pearl/sunbeam-stable/install.sh in function debug_capture on line 50 2019-08-28 17:58:47 UTC [ error] Environment creation failed! 2019-08-28 17:58:47 UTC [ error] Try re-running with -v or -d, or file an issue on Github.

I had tried installing some packages, especially libgcc somehow it picks appearing again

louiejtaylor commented 5 years ago

Great, thank you! I will work on reproducing this. One question in the meantime--do you have a .condarc file? (Usually located at ~/.condarc.) If so, would you mind pasting the contents here?

carolynePearl commented 5 years ago

channels:

louiejtaylor commented 5 years ago

Hmm, interesting. I know we've seen issues with channel order before that produced weird conda errors when solving for package dependencies. For the life of me, though, I don't remember whether bioconda or conda-forge is "supposed" to come first--pinging @ressy (as he did the work to track this down a while back) to see if he remembers? I think it's conda-forge first as that's what we have in the default sunbeam env, but I don't really know why.

Could you mv your .condarc file to a different name/location so that conda doesn't see it, and then try re-running the sunbeam install script? This should use the channel order that passes our automated tests (and may solve your problem!).

carolynePearl commented 5 years ago

  1. i have tried changing locations; (base) Pearl@ibr-svr-03:~$ cd sunbeam-stable/ (base) Pearl@ibr-svr-03:~/sunbeam-stable$ ./install.sh 2019-08-28 19:09:30 UTC [ info] Starting Sunbeam installation... 2019-08-28 19:09:30 UTC [ info] Conda path: /home/Pearl/miniconda3 2019-08-28 19:09:30 UTC [ info] Sunbeam src: /home/Pearl/sunbeam-stable 2019-08-28 19:09:30 UTC [ info] Sunbeam env: 'sunbeam' 2019-08-28 19:09:31 UTC [ info] Conda already installed. 2019-08-28 19:09:31 UTC [ info] Creating Sunbeam environment... ERROR urllib3.connection:_match_hostname(378): Certificate did not match expected hostname: repo.anaconda.com. Certificate: {'subject': ((('commonName', '.mak.ac.ug'),),), 'subjectAltName': [('DNS', '.mak.ac.ug')]}

  2. i have removed the channels and aded them again starting with conda-forge and then bioconda....i still get the same error

  3. i have installed my miniconda and removed all hidden files then re-run the script so that it installs its own conda; I still get the same error

ressy commented 5 years ago

Thanks @louiejtaylor and @carolynePearl for trying all this out.

According to bioconda's instructions we should have the channel order flipped, with conda-forge at the top, and that's what we're using in our latest development version. But the existing order has been working up until now in the stable version with the set of packages we have there. (When we release a new stable version that should finally be consistent and settled.) This only comes up when the same package (by name) is available from both channels but they're functionally different or have different dependencies so we want to make sure we get the right one.

Testing now it looks like a from-scratch install works on CircleCI for both stable and dev but then fails during testing because of missing samtools, so this may be another case of updated dependencies, maybe along with something different in carolynePearl's local environment. I'll see what's needed to get our tests passing again so we have a working case to compare with, and then I'm confident we can get things working for carolynePearl's instance too.

ressy commented 5 years ago

@louiejtaylor I suggested a new minor release in https://github.com/sunbeam-labs/sunbeam/pull/225 for the samtools problem. Let me know if that looks good and then I think we'll have a clear path to figuring out this one. These always seem to come in bunches!

louiejtaylor commented 5 years ago

@ressy it looks good to me!

louiejtaylor commented 5 years ago

Whoops I did not mean to close that :D

ressy commented 5 years ago

@carolynePearl could you try cloning this repository and running the command make inside the sunbeam-install-debug directory?

https://github.com/ressy/sunbeam-install-debug

This will install the latest stable Miniconda3 and Sunbeam straight into that directory and try to run the tests without relying on any other configuration files. If that works, then we can try to figure out what's different in ~/.condarc or ~/.bashrc, etc. Thanks for your patience!

carolynePearl commented 5 years ago

Thank you i will check it out first thing in the morning. Thanks alot

On Wed, 28 Aug 2019, 23:06 Jesse Connell, notifications@github.com wrote:

@carolynePearl https://github.com/carolynePearl could you try cloning this repository and running the command make inside the sunbeam-install-debug directory?

https://github.com/ressy/sunbeam-install-debug

This will install the latest stable Miniconda3 and Sunbeam straight into that directory and try to run the tests without relying on any other configuration files. If that works, then we can try to figure out what's different in ~/.condarc or ~/.bashrc, etc. Thanks for your patience!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/sunbeam-labs/sunbeam/issues/223?email_source=notifications&email_token=ANAXHBOGDTQ466FEAXPVZULQG3LCRA5CNFSM4IRDZPF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5MJ53I#issuecomment-525901549, or mute the thread https://github.com/notifications/unsubscribe-auth/ANAXHBPR7HPIVIPQWPH2BYTQG3LCRANCNFSM4IRDZPFQ .

carolynePearl commented 5 years ago

I have cloned the repository you provided and ran the make command:

Pearl@ibr-svr-03:~$ git clone https://github.com/ressy/sunbeam-install-debug.git Cloning into 'sunbeam-install-debug'... remote: Enumerating objects: 6, done. remote: Counting objects: 100% (6/6), done. remote: Compressing objects: 100% (5/5), done. remote: Total 37 (delta 1), reused 6 (delta 1), pack-reused 31 Unpacking objects: 100% (37/37), done. (base) Pearl@ibr-svr-03:~$ ls BIN_REFINEMENT METAWRAP Miniconda3-latest-Linux-x86_64.sh NCBI_tax projects BMTAGGER_INDEX MY_CHECKM_FOLDER NCBI_nt Tutorial sunbeam-install-debug (base) Pearl@ibr-svr-03:~$ cd sunbeam-install-debug/ (base) Pearl@ibr-svr-03:~/sunbeam-install-debug$ make git clone -b stable https://github.com/sunbeam-labs/sunbeam sunbeam-stable Cloning into 'sunbeam-stable'... remote: Enumerating objects: 47, done. remote: Counting objects: 100% (47/47), done. remote: Compressing objects: 100% (34/34), done. remote: Total 2747 (delta 15), reused 29 (delta 9), pack-reused 2700 Receiving objects: 100% (2747/2747), 1.23 MiB | 1.57 MiB/s, done. Resolving deltas: 100% (1607/1607), done. wget -q https://repo.anaconda.com/archive/Miniconda3-latest-Linux-x86_64.sh || wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh Makefile:9: recipe for target 'Miniconda3-latest-Linux-x86_64.sh' failed make: *** [Miniconda3-latest-Linux-x86_64.sh] Error 5 (base) Pearl@ibr-svr-03:~/sunbeam-install-debug$ ls Makefile README.md conda_wrapper.sh sunbeam-stable (base) Pearl@ibr-svr-03:~/sunbeam-install-debug$ tests/run_tests.bash -e sunbeam bash: tests/run_tests.bash: No such file or directory (base) Pearl@ibr-svr-03:~/sunbeam-install-debug$ tests/run_tests.bash -e sunbeam-stable/

carolynePearl commented 5 years ago

i haven't yet succeeded with the installation yet.

ressy commented 5 years ago

Thanks! That "Error 5" is coming from the download attempt for Miniconda3, I think, and according to wget's documentation exit status 5 means SSL verification failure. Come to think of it I remember seeing an SSL error for repo.anaconda.org from your logs yesterday:

ERROR urllib3.connection:_match_hostname(378):
Certificate did not match expected hostname: repo.anaconda.com.
Certificate: {'subject': ((('commonName', '.mak.ac.ug'),),), 'subjectAltName': [('DNS', '.mak.ac.ug')]}

Any chance your network configuration might be doing some kind of filtering or redirection pointing back to your own organization? (Is your computer located at Makerere University?)

One other thought: can you send the output of these two commands?

echo | openssl s_client -showcerts -connect repo.anaconda.org:443
tracepath repo.anaconda.org
carolynePearl commented 5 years ago

echo | openssl s_client -showcerts -connect repo.anaconda.org:443 CONNECTED(00000003) depth=3 C = SE, O = AddTrust AB, OU = AddTrust External TTP Network, CN = AddTrust External CA Root verify return:1 depth=2 C = GB, ST = Greater Manchester, L = Salford, O = COMODO CA Limited, CN = COMODO ECC Certification Authority verify return:1 depth=1 C = GB, ST = Greater Manchester, L = Salford, O = COMODO CA Limited, CN = COMODO ECC Domain Validation Secure Server CA 2 verify return:1 depth=0 OU = Domain Control Validated, OU = PositiveSSL Multi-Domain, CN = ssl383846.cloudflaressl.com verify return:1

Certificate chain 0 s:/OU=Domain Control Validated/OU=PositiveSSL Multi-Domain/CN=ssl383846.cloudflaressl.com i:/C=GB/ST=Greater Manchester/L=Salford/O=COMODO CA Limited/CN=COMODO ECC Domain Validation Secure Server CA 2 -----BEGIN CERTIFICATE----- MIIFBDCCBKmgAwIBAgIRAJ8VVh4U7Grq2+xH/BlX4D8wCgYIKoZIzj0EAwIwgZIx CzAJBgNVBAYTAkdCMRswGQYDVQQIExJHcmVhdGVyIE1hbmNoZXN0ZXIxEDAOBgNV BAcTB1NhbGZvcmQxGjAYBgNVBAoTEUNPTU9ETyBDQSBMaW1pdGVkMTgwNgYDVQQD Ey9DT01PRE8gRUNDIERvbWFpbiBWYWxpZGF0aW9uIFNlY3VyZSBTZXJ2ZXIgQ0Eg MjAeFw0xOTA2MjkwMDAwMDBaFw0yMDAxMDUyMzU5NTlaMGwxITAfBgNVBAsTGERv bWFpbiBDb250cm9sIFZhbGlkYXRlZDEhMB8GA1UECxMYUG9zaXRpdmVTU0wgTXVs dGktRG9tYWluMSQwIgYDVQQDExtzc2wzODM4NDYuY2xvdWRmbGFyZXNzbC5jb20w WTATBgcqhkjOPQIBBggqhkjOPQMBBwNCAARvMrjbGPAWiuxHqt+yOnWyWQTHXm6x aCVoRqUy7O9uBVfGYGo+gQ8WRSZmIWxWunIej23+bpXb2AJ1oWdMhRh4o4IDAzCC Av8wHwYDVR0jBBgwFoAUQAlhZ/C8g3FP3hIILG/U1Ct2PZYwHQYDVR0OBBYEFCGy uW2nZig6J9a0HZqg5zSXl+bVMA4GA1UdDwEB/wQEAwIHgDAMBgNVHRMBAf8EAjAA 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Server certificate subject=/OU=Domain Control Validated/OU=PositiveSSL Multi-Domain/CN=ssl383846.cloudflaressl.com issuer=/C=GB/ST=Greater Manchester/L=Salford/O=COMODO CA Limited/CN=COMODO ECC Domain Validation Secure Server CA 2

No client certificate CA names sent Peer signing digest: SHA256 Server Temp Key: ECDH, P-256, 256 bits

SSL handshake has read 3689 bytes and written 431 bytes

New, TLSv1/SSLv3, Cipher is ECDHE-ECDSA-AES128-GCM-SHA256 Server public key is 256 bit Secure Renegotiation IS supported Compression: NONE Expansion: NONE No ALPN negotiated SSL-Session: Protocol : TLSv1.2 Cipher : ECDHE-ECDSA-AES128-GCM-SHA256 Session-ID: 171DCAF7A5091EEAFD68AB8494AA4EA7893C151C5B119C3A5C9035D5A19FAD35 Session-ID-ctx: Master-Key: 8B1E13A37B1BB02EBC4F441360D55730A2DB0795A9000EF8EA72B7EEE057A56474DD6A41FCF0128968063F45917CAFE8 Key-Arg : None PSK identity: None PSK identity hint: None SRP username: None TLS session ticket lifetime hint: 64800 (seconds) TLS session ticket: 0000 - 95 93 28 ad 5e 2d cf 00-13 38 28 bc 05 30 c2 1e ..(.^-...8(..0.. 0010 - d0 3a b2 05 8d 2b 5a 16-25 ae 44 e1 91 6d 07 1a .:...+Z.%.D..m.. 0020 - 53 27 43 25 35 62 74 5e-0c b3 42 22 ee 13 d1 e5 S'C%5bt^..B".... 0030 - 52 7f d5 55 f6 8a a2 fb-d9 65 49 92 61 65 3a 7e R..U.....eI.ae:~ 0040 - a8 97 08 1e 36 6e ec 61-78 ed 7f 63 a1 68 7d bc ....6n.ax..c.h}. 0050 - cf b6 0e 8c d4 13 d7 06-c2 81 1e 8e 98 9f 08 c8 ................ 0060 - d2 04 c3 14 dc 78 03 74-bc 5d 65 1b cd 98 15 eb .....x.t.]e..... 0070 - 50 b6 9a 03 a2 85 00 3b-63 65 c6 96 0d 2f 79 a8 P......;ce.../y. 0080 - a6 a3 21 bf f2 23 ed e4-c2 d5 45 9f 40 43 47 71 ..!..#....E.@CGq 0090 - 85 1c e4 b7 78 2e 7d 50-51 51 f7 3c 1e 8d 0e ac ....x.}PQQ.<.... 00a0 - 25 5b d6 f7 fd 3a d7 c3-90 76 9e 00 d4 f5 ef 09 %[...:...v......

Start Time: 1567108439
Timeout   : 300 (sec)
Verify return code: 0 (ok)

DONE

carolynePearl commented 5 years ago

tracepath repo.anaconda.org 1?: [LOCALHOST] pmtu 1500 1: gateway 0.895ms 1: gateway 0.745ms 2: 196.43.132.37 2.007ms 3: 196.43.134.206 0.932ms 4: 196.43.189.17 3.642ms 5: stat.kla1.p-pe.renu.ac.ug 42.460ms 6: stat.kla1.peer-p.renu.ac.ug 3.607ms 7: ae0-300-ua-ug-kla1-01.ubuntunet.net 50.321ms 8: so0-0-0-ua-rw-kgl1-01.ubuntunet.net 15.083ms 9: gr0-2-10-ua-za-mtz1-01.ubuntunet.net 131.198ms 10: ge0-3-9-ua-za-mtz1-11.ubuntunet.net 65.884ms 11: no reply 12: no reply 13: no reply 14: no reply 15: no reply 16: no reply 17: no reply 18: no reply 19: no reply 20: no reply 21: no reply 22: no reply 23: no reply 24: no reply 25: no reply 26: no reply 27: no reply 28: no reply 29: no reply 30: no reply Too many hops: pmtu 1500 Resume: pmtu 1500

ressy commented 5 years ago

Thanks. That all actually looks fine. I wonder if it was a temporary networking problem that's now resolved? That's honestly just a guess, though. Could you try this command and let me know what it shows?

wget --method=HEAD -v -S https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
carolynePearl commented 5 years ago

Pearl@ibr-svr-03:~$ wget --method=HEAD -v -S https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh Spider mode enabled. Check if remote file exists. --2019-08-29 23:25:35-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh Resolving repo.anaconda.com (repo.anaconda.com)... 196.43.133.104 Connecting to repo.anaconda.com (repo.anaconda.com)|196.43.133.104|:443... connected. ERROR: no certificate subject alternative name matches requested host name 'repo.anaconda.com'. To connect to repo.anaconda.com insecurely, use `--no-check-certificate'.

ressy commented 5 years ago

Wait a minute, 196.43.133.104? That's not the right IP address for repo.anaconda.com. That points back to the IT group for Makerere, apparently:

$ host 196.43.133.104
104.133.43.196.in-addr.arpa domain name pointer dicts.mak.ac.ug.

For example when I try that wget command, I see this:

Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.131.3|:443... connected.

Instead of:

Connecting to repo.anaconda.com (repo.anaconda.com)|196.43.133.104|:443... connected.

I think that's the problem. I'd suggest contacting DICTS and showing these logs, especially that last one with 196.43.133.104 showing up as repo.anaconda.com. I expect they can make corrections in DNS so this works as expected.

louiejtaylor commented 5 years ago

Based on the fact that this seems to be a problem with the host institution's DNS rather than anything Sunbeam-related, I'm inclined to close this issue for now.

@ressy, feel free to reopen if you disagree.

@carolynePearl, if your institution solves the DNS issues and you're still having trouble installing Sunbeam, feel free to either reopen this issue by adding another comment, or to open a new issue if you feel that would be more appropriate. Good luck!