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richelbilderbeek / razzo

Research project by Giovanni Laudanno and Richel J.C. Bilderbeek
GNU General Public License v3.0
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Get test run to work again #371

Closed richelbilderbeek closed 4 years ago

richelbilderbeek commented 4 years ago 
p230198@peregrine:razzo_project cat run_r_cmd_8944007.log 

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/1/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: Expect 'End;' (BEAST2) or 'END;' (ape::write.nexus) at the end of .trees file 
Actual value: tree STATE_62 = ((((1:2.6836473752124332,13:2.6836473752124332):0.6498330382739441,(2:1.7031644650477895,(4:1.3098987793474899,(6:0.3958427817327079,10:0.3958427817327079):0.914055997614782):0.3932656857002996):1.6303159484385878):0.006575891632751407,((((3:0.17891618621863536,8:0.17891618621863536):1.241301955041191,(5:1.0714832488997974,14:1.0714832488997974):0.3487348923600291):0.7273730229953281,11:2.1475911642551546):1.0999539909079115,12:3.247545155163066):0.09251114995606269):4.6596725150161875,(7:0.29079455059826703,9:0.29079455059826703):7.708934269537049):0.0;
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evidenc
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 8944007 for user 'p230198'
Finished at: Mon Dec  9 12:44:56 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node211
Cores               : 1
State               : FAILED
Submit              : 2019-12-09T12:44:15
Start               : 2019-12-09T12:44:15
End                 : 2019-12-09T12:44:56
Reserved walltime   : 2-12:00:00
Used walltime       :   00:00:41
Used CPU time       :   00:00:36 (efficiency: 90.02%)
% User (Computation): 95.62%
% System (I/O)      :  4.38%
Mem reserved        : 10G/node
Max Mem used        : 325.84M (pg-node211)
Max Disk Write      : 133.12K (pg-node211)
Max Disk Read       : 3.19M (pg-node211)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################

and

p230198@peregrine:razzo_project cat run_r_cmd_8944008.log 

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: n_trees_in_file == n_trees_in_output is not TRUE
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen_evidence.xml.state2NAFALSETRUE/home/p230198/.local/share/beast/bin/beastFALSE
inference_model: list(name = "JC69", id = NA, gamma_site_model = list(gamma_cat_count = "0", gamma_shape = "1.0", prop_invariant = "0.0", gamma_shape_prior_distr = NA, freq_equilibrium = "estimated"))list(name = "strict", id = NA, clock_rate_param = list(name = "clock_rate", id = NA, value = "1.0", estimate = FALSE), clock_rate_distr = list(name = "uniform", id = NA, upper = Inf))list(name = "birth_death", id = NA, birth_rate_distr = list(name = "uniform", id = NA, upper = Inf), death_rate_distr = list(name = "uniform", id = NA, upper = Inf))li
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 8944008 for user 'p230198'
Finished at: Mon Dec  9 12:45:20 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node211
Cores               : 1
State               : FAILED
Submit              : 2019-12-09T12:44:15
Start               : 2019-12-09T12:44:15
End                 : 2019-12-09T12:45:20
Reserved walltime   : 2-12:00:00
Used walltime       :   00:01:05
Used CPU time       :   00:01:00 (efficiency: 93.72%)
% User (Computation): 97.28%
% System (I/O)      :  2.72%
Mem reserved        : 10G/node
Max Mem used        : 334.44M (pg-node211)
Max Disk Write      : 133.12K (pg-node211)
Max Disk Read       : 3.19M (pg-node211)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################
richelbilderbeek commented 4 years ago 
richel@sonic:~/GitHubs$ egrep -R "Could not estimate the marginal likelihood" --include=*.R
mcbette/R/est_marg_lik.R:        "Could not estimate the marginal likelihood. \n",
richelbilderbeek commented 4 years ago

Perhaps the root cause:

richel@sonic:~/GitHubs$ egrep -R "n_trees_in_file == n_trees_in_output"
tracerer/R/parse_beast_trees.R:  testit::assert(n_trees_in_file == n_trees_in_output)
babette/R/bbt_run_from_model.R:  testit::assert(n_trees_in_file == n_trees_in_output)
richelbilderbeek commented 4 years ago 
230198@peregrine:razzo_project cat run_r_cmd_89775*.log 

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/1/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: Expect 'End;' (BEAST2) or 'END;' (ape::write.nexus) at the end of .trees file 
Actual value: tree STATE_58 = (((((1:2.166150524106325,13:2.166150524106325):0.7827797291347007,12:2.9489302532410258):0.028064256667378107,(2:1.7648089444813044,(4:1.443127787811669,(6:0.20789000181260223,10:0.20789000181260223):1.2352377859990669):0.32168115666963537):1.2121855654270994):0.024276685208170612,(((3:0.09152130083612744,8:0.09152130083612744):1.2576990478746901,(5:0.9641532558944922,14:0.9641532558944922):0.38506709281632545):0.5202067803847912,11:1.8694271290956088):1.1318440660209657):4.998700599644323,(7:0.35519322637241213,9:0.35519322637241213):7.644778568388485):0.0;
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evi
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 8977569 for user 'p230198'
Finished at: Thu Dec 12 12:02:23 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node214
Cores               : 1
State               : FAILED
Submit              : 2019-12-12T12:01:41
Start               : 2019-12-12T12:01:42
End                 : 2019-12-12T12:02:22
Reserved walltime   : 2-12:00:00
Used walltime       :   00:00:40
Used CPU time       :   00:00:36 (efficiency: 91.67%)
% User (Computation): 95.25%
% System (I/O)      :  4.75%
Mem reserved        : 10G/node
Max Mem used        : 328.80M (pg-node214)
Max Disk Write      : 133.12K (pg-node214)
Max Disk Read       : 3.19M (pg-node214)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: n_trees_in_file == n_trees_in_output is not TRUE
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen_evidence.xml.state2NAFALSETRUE/home/p230198/.local/share/beast/bin/beastFALSE
inference_model: list(name = "JC69", id = NA, gamma_site_model = list(gamma_cat_count = "0", gamma_shape = "1.0", prop_invariant = "0.0", gamma_shape_prior_distr = NA, freq_equilibrium = "estimated"))list(name = "strict", id = NA, clock_rate_param = list(name = "clock_rate", id = NA, value = "1.0", estimate = FALSE), clock_rate_distr = list(name = "uniform", id = NA, upper = Inf))list(name = "birth_death", id = NA, birth_rate_distr = list(name = "uniform", id = NA, upper = Inf), death_rate_distr = list(name = "uniform", id = NA, upper = Inf))li
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 8977570 for user 'p230198'
Finished at: Thu Dec 12 12:02:50 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node214
Cores               : 1
State               : FAILED
Submit              : 2019-12-12T12:01:41
Start               : 2019-12-12T12:01:42
End                 : 2019-12-12T12:02:50
Reserved walltime   : 2-12:00:00
Used walltime       :   00:01:08
Used CPU time       :   00:01:03 (efficiency: 93.98%)
% User (Computation): 97.19%
% System (I/O)      :  2.81%
Mem reserved        : 10G/node
Max Mem used        : 331.85M (pg-node214)
Max Disk Write      : 133.12K (pg-node214)
Max Disk Read       : 3.19M (pg-node214)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################
richelbilderbeek commented 4 years ago 
p230198@peregrine:razzo_project cat run_r_cmd_89795*

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/1/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: Expect 'End;' (BEAST2) or 'END;' (ape::write.nexus) at the end of .trees file 
Actual value: tree STATE_61 = (((((1:2.5222032643214405,13:2.5222032643214405):0.4668862628055681,(((3:0.148365544458197,8:0.148365544458197):1.4243165658542638,(5:1.3799997797038261,14:1.3799997797038261):0.1926823306086347):0.7851181977105228,11:2.3578003080229837):0.6312892191040249):0.06828398344693509,12:3.0573735105739437):0.4134778715086158,(2:1.924625238934493,(4:1.512857845959948,(6:0.33869858901169253,10:0.33869858901169253):1.1741592569482555):0.4117673929745451):1.5462261431480664):4.528877438052756,(7:0.16933084284654,9:0.16933084284654):7.830397977288777):0.0;
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evidence.xml.stat
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 8979559 for user 'p230198'
Finished at: Thu Dec 12 12:28:18 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node214
Cores               : 1
State               : FAILED
Submit              : 2019-12-12T12:27:38
Start               : 2019-12-12T12:27:39
End                 : 2019-12-12T12:28:18
Reserved walltime   : 2-12:00:00
Used walltime       :   00:00:39
Used CPU time       :   00:00:36 (efficiency: 93.59%)
% User (Computation): 95.37%
% System (I/O)      :  4.63%
Mem reserved        : 10G/node
Max Mem used        : 335.81M (pg-node214)
Max Disk Write      : 133.12K (pg-node214)
Max Disk Read       : 3.19M (pg-node214)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: object 'inference_model' not found
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen_evidence.xml.state2NAFALSETRUE/home/p230198/.local/share/beast/bin/beastFALSE
inference_model: list(name = "JC69", id = NA, gamma_site_model = list(gamma_cat_count = "0", gamma_shape = "1.0", prop_invariant = "0.0", gamma_shape_prior_distr = NA, freq_equilibrium = "estimated"))list(name = "strict", id = NA, clock_rate_param = list(name = "clock_rate", id = NA, value = "1.0", estimate = FALSE), clock_rate_distr = list(name = "uniform", id = NA, upper = Inf))list(name = "birth_death", id = NA, birth_rate_distr = list(name = "uniform", id = NA, upper = Inf), death_rate_distr = list(name = "uniform", id = NA, upper = Inf))list(name = NA, 
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 8979560 for user 'p230198'
Finished at: Thu Dec 12 12:28:42 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node214
Cores               : 1
State               : FAILED
Submit              : 2019-12-12T12:27:38
Start               : 2019-12-12T12:27:39
End                 : 2019-12-12T12:28:42
Reserved walltime   : 2-12:00:00
Used walltime       :   00:01:03
Used CPU time       :   00:01:00 (efficiency: 96.08%)
% User (Computation): 97.12%
% System (I/O)      :  2.88%
Mem reserved        : 10G/node
Max Mem used        : 333.15M (pg-node214)
Max Disk Write      : 133.12K (pg-node214)
Max Disk Read       : 3.19M (pg-node214)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################
richelbilderbeek commented 4 years ago 
p230198@peregrine:razzo_project cat run_r_cmd_897960*

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/1/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: Expect 'End;' (BEAST2) or 'END;' (ape::write.nexus) at the end of .trees file. 
Actual value: 'tree STATE_63 = ((((1:2.370341722004589,13:2.370341722004589):0.3873429914476132,(2:1.3571204948229938,(4:1.3492473971994121,(6:0.13807698460970969,10:0.13807698460970969):1.2111704125897025):0.007873097623581682):1.4005642186292082):0.05377902387074451,((((3:0.16227395156622654,8:0.16227395156622654):1.2178279052765282,(5:0.9791292948697641,14:0.9791292948697641):0.4009725619729907):0.49463667398725186,11:1.8747385308300066):0.8872863794749353,12:2.762024910304942):0.049438827018004616):5.18826508281237,(7:0.18209095086638263,9:0.18209095086638263):7.817637869268934):0.0;'. 
Filename: 'mbd_evidence.trees'
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_projec
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 8979604 for user 'p230198'
Finished at: Thu Dec 12 12:59:10 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node214
Cores               : 1
State               : FAILED
Submit              : 2019-12-12T12:58:29
Start               : 2019-12-12T12:58:29
End                 : 2019-12-12T12:59:10
Reserved walltime   : 2-12:00:00
Used walltime       :   00:00:41
Used CPU time       :   00:00:36 (efficiency: 89.56%)
% User (Computation): 95.01%
% System (I/O)      :  4.99%
Mem reserved        : 10G/node
Max Mem used        : 335.30M (pg-node214)
Max Disk Write      : 133.12K (pg-node214)
Max Disk Read       : 3.19M (pg-node214)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: Different number of trees parsed than expected. n_trees_in_file: 162. n_trees_in_output: 67. filename: mbd_evidence.trees. File content: #NEXUS

Begin taxa;
        Dimensions ntax=9;
                Taxlabels
                        t12
                        t14
                        t17
                        t18
                        t19
                        t2
                        t20
                        t21
                        t7
                        ;
End;
Begin trees;
        Translate
                   1 t12,
                   2 t14,
                   3 t17,
                   4 t18,
                   5 t19,
                   6 t2,
                   7 t20,
                   8 t21,
                   9 t7
;
tree STATE_0 = (((((1:0.7982885103376582,8:0.7982885103376582):0.04703513311996932,3:0.8453236434576276):1.464998835402068,6:2.3103224788596957):1.6974981662349866,7:4.007820645094682):3.991480501031626,((2:1.179932318740965,4:1.179932318740965):0.14322616315509062,(5:0.3587811633659665,9:0.3587811633659665):0.964377318530089):6.676142664230253):0.0;
tree STATE_1 = ((((((1:0.0502456589025746,5:0.0502456589025746):0.09221787121392705,4:0.14246353011650165):1.1739542192319743,7:1.3164177493484759):0.7036849299432404,9:2.020102679291716
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
In readLines(filename) :
  incomplete final line found on 'mbd_evidence.trees'
Execution halted

###############################################################################
Peregrine Cluster
Job 8979605 for user 'p230198'
Finished at: Thu Dec 12 12:59:33 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node214
Cores               : 1
State               : FAILED
Submit              : 2019-12-12T12:58:29
Start               : 2019-12-12T12:58:29
End                 : 2019-12-12T12:59:33
Reserved walltime   : 2-12:00:00
Used walltime       :   00:01:04
Used CPU time       :   00:00:59 (efficiency: 93.37%)
% User (Computation): 96.91%
% System (I/O)      :  3.09%
Mem reserved        : 10G/node
Max Mem used        : 331.17M (pg-node214)
Max Disk Write      : 133.12K (pg-node214)
Max Disk Read       : 3.19M (pg-node214)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################
richelbilderbeek commented 4 years ago

Hmmm, updating BEAST2 does not work...

richelbilderbeek commented 4 years ago

Last state of affairs:

p230198@peregrine:razzo_project ls
1_install_razzo.log           fig_mean_esses.png                       fig_states.png                README.md
2_create_parameter_files.log  fig_mean_n_taxa.png                      LICENSE                       run_r_cmd_9048428.log
3_run_razzo.log               fig_n_mb_species.png                     mbd_evidence.log              run_r_cmd_9048429.log
data                          fig_runtime_per_n_taxa.png               mbd_evidence.posterior.trees  scripts
DESCRIPTION                   fig_run_times_boxplot.png                mbd_evidence.trees            verdict.csv
detailed_overview.csv         fig_run_times_per_crown_age_grouped.png  overview.csv                  verdict.md
fig_esses.png                 fig_run_times_per_crown_age.png          overview.md
fig_f_mb_species.png          fig_run_times.png                        pics
p230198@peregrine:razzo_project cat run_r_cmd_904842*

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/1/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: Expect 'End;' (BEAST2) or 'END;' (ape::write.nexus) at the end of .trees file. 
Actual value: 'tree STATE_61 = (((((1:2.5222032643214405,13:2.5222032643214405):0.4668862628055681,(((3:0.148365544458197,8:0.148365544458197):1.4243165658542638,(5:1.3799997797038261,14:1.3799997797038261):0.1926823306086347):0.7851181977105228,11:2.3578003080229837):0.6312892191040249):0.06828398344693509,12:3.0573735105739437):0.4134778715086158,(2:1.924625238934493,(4:1.512857845959948,(6:0.33869858901169253,10:0.33869858901169253):1.1741592569482555):0.4117673929745451):1.5462261431480664):4.528877438052756,(7:0.16933084284654,9:0.16933084284654):7.830397977288777):0.0;'. 
Filename: 'mbd_evidence.trees'
fasta_filename: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_evidence.fasta
beast2_options: /home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/mbd_gen_evidence.xml/home/p230198/GitHubs/razzo_project/data/0.2-0.
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

###############################################################################
Peregrine Cluster
Job 9048428 for user 'p230198'
Finished at: Sun Dec 15 13:19:11 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node211
Cores               : 1
State               : FAILED
Submit              : 2019-12-15T13:18:28
Start               : 2019-12-15T13:18:29
End                 : 2019-12-15T13:19:11
Reserved walltime   : 2-12:00:00
Used walltime       :   00:00:42
Used CPU time       :   00:00:37 (efficiency: 88.50%)
% User (Computation): 95.11%
% System (I/O)      :  4.89%
Mem reserved        : 10G/node
Max Mem used        : 331.10M (pg-node211)
Max Disk Write      : 133.12K (pg-node211)
Max Disk Read       : 3.19M (pg-node211)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################

The following have been reloaded with a version change:
  1) GCCcore/8.2.0 => GCCcore/6.4.0
  2) GMP/6.1.2-GCCcore-8.2.0 => GMP/6.1.2-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.6-GCCcore-8.2.0 => expat/2.2.5-GCCcore-6.4.0

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: Different number of trees parsed than expected. n_trees_in_file: 160. n_trees_in_output: 65. filename: mbd_evidence.trees. File content: #NEXUS

Begin taxa;
        Dimensions ntax=14;
                Taxlabels
                        t1
                        t10
                        t11
                        t12
                        t13
                        t14
                        t15
                        t16
                        t3
                        t5
                        t6
                        t7
                        t8
                        t9
                        ;
End;
Begin trees;
        Translate
                   1 t1,
                   2 t10,
                   3 t11,
                   4 t12,
                   5 t13,
                   6 t14,
                   tree STATE_0 = (((((1:0.7982885103376582,8:0.7982885103376582):0.04703513311996932,3:0tree STATE_0 = ((1:4.977424343036875,(5:0.08987551658046206,11:0.08987551658046206):4.887548826456413):3.0208361124781407,(((((2:0.5054442887803194,13:0.5054442887803194):0.04274311890977711,12:0.5481874076900966):0.5893456983057705,6:1.137533105995867):1.17143865942tree STATE_1 = ((((((1:0.0502456589025746,5:0.0502456589025746):0.09221787121392705,4:0.14246353011650165):1.1739542192319743,7:1.3164177493484759):0.7036849299432404,9:2.020102679291716
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
In readLines(filename) :
  incomplete final line found on 'mbd_evidence.trees'
Execution halted

###############################################################################
Peregrine Cluster
Job 9048429 for user 'p230198'
Finished at: Sun Dec 15 13:19:35 CET 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : gelifes
Nodes               : pg-node211
Cores               : 1
State               : FAILED
Submit              : 2019-12-15T13:18:28
Start               : 2019-12-15T13:18:29
End                 : 2019-12-15T13:19:35
Reserved walltime   : 2-12:00:00
Used walltime       :   00:01:06
Used CPU time       :   00:01:01 (efficiency: 92.81%)
% User (Computation): 96.89%
% System (I/O)      :  3.10%
Mem reserved        : 10G/node
Max Mem used        : 333.89M (pg-node211)
Max Disk Write      : 133.12K (pg-node211)
Max Disk Read       : 3.19M (pg-node211)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################
richelbilderbeek commented 4 years ago

Will run locally now...

richelbilderbeek commented 4 years ago

running

richelbilderbeek commented 4 years ago

Works well locally ...

richel@sonic:~/GitHubs/razzo_project$ ./scripts/3_run_razzo.sh 
./scripts/3_run_razzo.sh: line 21: module: command not found
./scripts/3_run_razzo.sh: line 22: module: command not found
Host name: sonic
Working from laptop
./data/0.2-0.15-1-0.1/1/parameters.RDa
./scripts/run_r_cmd: line 16: module: command not found
./scripts/run_r_cmd: line 17: module: command not found
Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/1/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
  tree inference_model inference_model_weight site_model clock_model
1 true      generative        0.9999994907966       JC69      strict
2 true       candidate        0.0000005072543        HKY      strict
3 twin      generative        1.0000000000000       JC69      strict
4 twin       candidate        0.0000000000000        HKY      strict
   tree_prior   error_1   error_2   error_3   error_4
1 birth_death 0.2447334 0.3022202 0.3022356 0.3023344
2        yule 0.2447334 0.3124712 0.3145045 0.3115535
3 birth_death 0.2672307 0.3254771 0.3283272 0.3254156
4        yule 0.2672307 0.2652065 0.2667765 0.2655575
./data/0.2-0.15-1-0.1/2/parameters.RDa
./scripts/run_r_cmd: line 16: module: command not found
./scripts/run_r_cmd: line 17: module: command not found
Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
  tree inference_model inference_model_weight site_model clock_model
1 true      generative         1.000000000000       JC69      strict
2 true       candidate         0.000000000000        HKY      strict
3 twin      generative         0.999990467498       JC69      strict
4 twin       candidate         0.000009532502        HKY      strict
   tree_prior    error_1   error_2   error_3   error_4
1 birth_death 0.07195127 0.1218919 0.1242286 0.1233012
2        yule 0.07195127 0.1317896 0.1308977 0.1349622
3 birth_death 0.16913203 0.1940720 0.1834526 0.1787113
4        yule 0.16913203 0.1961072 0.1753339 0.1731899
richelbilderbeek commented 4 years ago

Maybe this is it:

p230198@peregrine:razzo_project cat 1_install_razzo.log 

[...]

babette      (62ef1b080... -> 48e5fee3e...) [GitHub]
callr        (3.3.2        -> 3.4.0       ) [CRAN]
mbd.TaxaA... (3353f8fcc... -> 8fd3bd9de...) [GitHub]
quantreg     (5.52         -> 5.54        ) [CRAN]
raket        (03502fc93... -> 95a687a74...) [GitHub]
testthat     (2.3.0        -> 2.3.1       ) [CRAN]
AlgDesign    (1.1-7.3      -> 1.2.0       ) [CRAN]
[...]
graphlayouts (NA           -> 0.5.0       ) [CRAN]
TFisher      (NA           -> 0.2.0       ) [CRAN]
mutoss       (NA           -> 0.1-12      ) [CRAN]
fastmap      (NA           -> 1.0.1       ) [CRAN]
rex          (NA           -> 1.1.2       ) [CRAN]
Skipping 6 packages not available: expoRkit, biom, cghFLasso, lqa, uniqueAtomMat, multtest
Installing 212 packages: callr, quantreg, testthat, AlgDesign, asnipe, BayesianTools, bayesm, BB, BDgraph, BH, bio3d, blob, bnlearn, bridgesampling, broom, calibrate, car, carData, caTools, chron, circlize, classInt, clipr, clustree, coin, compositions, cowplot, crul, cubature, data.table, DBI, ddalpha, deldir, dendextend, Deriv, devtools, DHARMa, doMC, doParallel, doSNOW, DT, dtangle, DTRreg, dtw, e1071, energy, extRemes, FactoMineR, feather, fields, foreach, forecast, fracdiff, future, gamlss, gamlss.dist, gee, geepack, geometry, ggforce, ggraph, ggvis, GillespieSSA, glasso, gllvm, glmnet, GlobalOptions, globals, gmm, goftest, h2o, haven, hdf5r, hexbin, Hmisc, hms, htmlTable, htmltools, htmlwidgets, httpuv, httr, huge, iterators, jomo, jpeg, kernlab, kohonen, ks, labdsv, lambda.r, later, lava, lavaan, libcoin, limSolve, liquidSVM, listenv, logspline, lpSolve, maptools, matrixStats, mclust, MCMCpack, mediation, metap, mice, miscTools, mlogit, mlr, modelr, mpath, msm, multcomp, multicool, network, openssl, openxlsx, optmatch, optparse, ordinal, ParamHelpers, partykit, plotly, pls, plyr, polspline, pracma, pROC, prodlim, promises, pulsar, pvclust, qgraph, qrnn, R.cache, R.oo, R.rsp, R.utils, randomForestSRC, raster, RcppArmadillo, RcppEigen, RcppGSL, Rdpack, recipes, rematch2, reticulate, rgl, ritis, RItools, RJSONIO, rlecuyer, rmarkdown, rms, RNeXML, rootSolve, rotl, roxygen2, rrcov, RSNNS, RSQLite, rversions, rvest, RWeka, RWekajars, SDMTools, seewave, selectr, shiny, slam, sna, solrium, sp, spam, SparseM, spatstat, spatstat.utils, spData, strucchange, SuperLearner, svd, sys, taxize, tidyverse, timereg, tinytex, tm, TraMineR, TTR, units, uroot, usethis, vegan, VGAM, vioplot, visNetwork, webshot, whisker, worrms, WriteXLS, XML, zip, zoo, mvnfast, covr, linprog, graphlayouts, TFisher, mutoss, fastmap, rex, multtest
Installing packages into ‘/home/p230198/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Error: (converted from warning) package ‘multtest’ is not available (for R version 3.6.1)
Execution halted

Especially:

Error: (converted from warning) package ‘multtest’ is not available (for R version 3.6.1)

Installing it afresh from BioConductor.

richelbilderbeek commented 4 years ago

Reached my GitHub limit for today :disappointed:

richelbilderbeek commented 4 years ago

Newest error:

checking for matching HDF5 Fortran wrapper... /usr/bin/h5fc
Found hdf5 with version: 1.8.12
configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.13 is installed
ERROR: configuration failed for package ‘hdf5r’
* removing ‘/home/p230198/R/x86_64-pc-linux-gnu-library/3.6/hdf5r’
Error in i.p(...) : 
  (converted from warning) installation of package ‘hdf5r’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
richelbilderbeek commented 4 years ago

AFAICS, I fixed the install of HDF5 by:

p230198@peregrine:razzo_project cat scripts/1_install_razzo.sh 
[...]
module load R HDF5/1.10.1-foss-2018a

Results in:

p230198@peregrine:razzo_project cat 1_install_razzo.log 

The following have been reloaded with a version change:
  1) GCCcore/7.3.0 => GCCcore/6.4.0
  2) HDF5/1.10.2-intel-2018b => HDF5/1.10.1-foss-2018a
  3) Szip/2.1.1-GCCcore-7.3.0 => Szip/2.1.1-GCCcore-6.4.0
  4) zlib/1.2.11-GCCcore-7.3.0 => zlib/1.2.11-GCCcore-6.4.0

Installing package into ‘/home/p230198/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Calls: install.packages -> startsWith -> contrib.url
Execution halted
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installation path not writeable, unable to update packages: AlgDesign, asnipe,
  backports, BayesianTools, bayesm, BB, BDgraph, BH, bio3d, blob, bnlearn,
  bridgesampling, broom, calibrate, callr, car, carData, caTools, chron,
  circlize, classInt, cli, clipr, clustree, coin, compositions, cowplot, crul,
  cubature, curl, data.table, DBI, ddalpha, deldir, dendextend, Deriv, deSolve,
  devtools, DHARMa, digest, doMC, doParallel, doSNOW, DT, dtangle, DTRreg, dtw,
  e1071, ellipsis, energy, extRemes, FactoMineR, farver, feather, fields, FME,
  foreach, forecast, foreign, fracdiff, future, gamlss, gamlss.dist, gee,
  geepack, geometry, ggforce, ggplot2, ggraph, ggvis, GillespieSSA, glasso,
  gllvm, glmnet, GlobalOptions, globals, gmm, goftest, h2o, haven, hdf5r,
  hexbin, Hmisc, hms, htmlTable, htmltools, htmlwidgets, httpuv, httr, huge,
  igraph, iterators, jomo, jpeg, kernlab, KernSmooth, knitr, kohonen, ks,
  labdsv, lambda.r, later, lava, lavaan, libcoin, limSolve, liquidSVM, listenv,
  logspline, lpSolve, magick, maptools, markdown, Matrix, matrixStats, mclust,
  MCMCpack, mediation, metap, mgcv, mice, mime, miscTools, mlogit, mlr, modelr,
  mpath, msm, multcomp, multicool, network, nlme, OceanView, openssl, openxlsx,
  optmatch, optparse, ordinal, ParamHelpers, partykit, pbapply, pkgbuild,
  pkgconfig, plot3D, plotly, plotrix, pls, plyr, polspline, pracma, pROC,
  processx, prodlim, promises, pulsar, purrr, pvclust, qgraph, qrnn, quadprog,
  quantreg, R.cache, R.oo, R.rsp, R.utils, R6, randomForestSRC, raster, Rcpp,
  RcppArmadillo, RcppEigen, RcppGSL, Rdpack, recipes, rematch2, reticulate,
  rgl, ritis, RItools, RJSONIO, rlang, rlecuyer, rmarkdown, rms, RNeXML,
  rootSolve, rotl, roxygen2, rrcov, RSNNS, RSQLite, rversions, rvest, RWeka,
  RWekajars, scales, SDMTools, seewave, segmented, selectr, seqinr, shiny,
  slam, sna, solrium, sp, spam, SparseM, spatstat, spatstat.utils, spData,
  strucchange, SuperLearner, survival, svd, sys, taxize, testthat, tidyr,
  tidyverse, timereg, tinytex, tm, TraMineR, TTR, units, uroot, usethis, vctrs,
  vegan, VGAM, vioplot, visNetwork, webshot, whisker, worrms, WriteXLS, xfun,
  XML, xml2, zip, zoo
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installation path not writeable, unable to update packages: AlgDesign, asnipe,
  backports, BayesianTools, bayesm, BB, BDgraph, BH, bio3d, blob, bnlearn,
  bridgesampling, broom, calibrate, callr, car, carData, caTools, chron,
  circlize, classInt, cli, clipr, clustree, coin, compositions, cowplot, crul,
  cubature, curl, data.table, DBI, ddalpha, deldir, dendextend, Deriv, deSolve,
  devtools, DHARMa, digest, doMC, doParallel, doSNOW, DT, dtangle, DTRreg, dtw,
  e1071, ellipsis, energy, extRemes, FactoMineR, farver, feather, fields, FME,
  foreach, forecast, foreign, fracdiff, future, gamlss, gamlss.dist, gee,
  geepack, geometry, ggforce, ggplot2, ggraph, ggvis, GillespieSSA, glasso,
  gllvm, glmnet, GlobalOptions, globals, gmm, goftest, h2o, haven, hdf5r,
  hexbin, Hmisc, hms, htmlTable, htmltools, htmlwidgets, httpuv, httr, huge,
  igraph, iterators, jomo, jpeg, kernlab, KernSmooth, knitr, kohonen, ks,
  labdsv, lambda.r, later, lava, lavaan, libcoin, limSolve, liquidSVM, listenv,
  logspline, lpSolve, magick, maptools, markdown, Matrix, matrixStats, mclust,
  MCMCpack, mediation, metap, mgcv, mice, mime, miscTools, mlogit, mlr, modelr,
  mpath, msm, multcomp, multicool, network, nlme, OceanView, openssl, openxlsx,
  optmatch, optparse, ordinal, ParamHelpers, partykit, pbapply, pkgbuild,
  pkgconfig, plot3D, plotly, plotrix, pls, plyr, polspline, pracma, pROC,
  processx, prodlim, promises, pulsar, purrr, pvclust, qgraph, qrnn, quadprog,
  quantreg, R.cache, R.oo, R.rsp, R.utils, R6, randomForestSRC, raster, Rcpp,
  RcppArmadillo, RcppEigen, RcppGSL, Rdpack, recipes, rematch2, reticulate,
  rgl, ritis, RItools, RJSONIO, rlang, rlecuyer, rmarkdown, rms, RNeXML,
  rootSolve, rotl, roxygen2, rrcov, RSNNS, RSQLite, rversions, rvest, RWeka,
  RWekajars, scales, SDMTools, seewave, segmented, selectr, seqinr, shiny,
  slam, sna, solrium, sp, spam, SparseM, spatstat, spatstat.utils, spData,
  strucchange, SuperLearner, survival, svd, sys, taxize, testthat, tidyr,
  tidyverse, timereg, tinytex, tm, TraMineR, TTR, units, uroot, usethis, vctrs,
  vegan, VGAM, vioplot, visNetwork, webshot, whisker, worrms, WriteXLS, xfun,
  XML, xml2, zip, zoo
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'multtest'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/multtest_2.42.0.tar.gz'
Content type 'application/x-gzip' length 1294308 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

* installing *source* package ‘multtest’ ...
** using staged installation
** libs
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c Rpack.c -o Rpack.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c VScount.c -o VScount.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c block_sampling_fixed.c -o block_sampling_fixed.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c bootloop.c -o bootloop.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c mt.c -o mt.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c pairt_sampling.c -o pairt_sampling.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c random.c -o random.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c sampling.c -o sampling.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c sampling_fixed.c -o sampling_fixed.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c stat_func.c -o stat_func.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include -DUSEDOUBLE -fpic  -O2 -ftree-vectorize -fno-math-errno  -c stat_order.c -o stat_order.o
gcc -shared -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -L/software/software/GCCcore/6.4.0/lib64 -L/software/software/GCCcore/6.4.0/lib -L/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib -L/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/lib -L/software/software/FFTW/3.3.7-gompi-2018a/lib -L/software/software/X11/20180131-GCCcore-6.4.0/lib -L/software/software/Mesa/17.3.6-foss-2018a/lib -L/software/software/libGLU/9.0.0-foss-2018a/lib -L/software/software/cairo/1.14.12-GCCcore-6.4.0/lib -L/software/software/libreadline/7.0-GCCcore-6.4.0/lib -L/software/software/ncurses/6.1-GCCcore-6.4.0/lib -L/software/software/bzip2/1.0.6-GCCcore-6.4.0/lib -L/software/software/XZ/5.2.3-GCCcore-6.4.0/lib -L/software/software/zlib/1.2.11-GCCcore-6.4.0/lib -L/software/software/SQLite/3.21.0-GCCcore-6.4.0/lib -L/software/software/PCRE/8.41-GCCcore-6.4.0/lib -L/software/software/libpng/1.6.34-GCCcore-6.4.0/lib -L/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/lib -L/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/lib -L/software/software/Java/1.8.0_192/lib -L/software/software/Tk/8.6.8-foss-2018a/lib -L/software/software/cURL/7.58.0-GCCcore-6.4.0/lib -L/software/software/libxml2/2.9.7-GCCcore-6.4.0/lib -L/software/software/GMP/6.1.2-GCCcore-6.4.0/lib -L/software/software/NLopt/2.4.2-foss-2018a/lib -L/software/software/libsndfile/1.0.28-GCCcore-6.4.0/lib -L/software/software/ICU/61.1-GCCcore-6.4.0/lib -L/software/software/HDF5/1.10.1-foss-2018a/lib -L/software/software/UDUNITS/2.2.26-foss-2018a/lib -L/software/software/GSL/2.4-GCCcore-6.4.0/lib -L/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/lib -o multtest.so Rpack.o VScount.o block_sampling_fixed.o bootloop.o mt.o pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o sampling_fixed.o stat_func.o stat_order.o -lm -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -lR
installing to /home/p230198/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-multtest/00new/multtest/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (multtest)

The downloaded source packages are in
        ‘/local/tmp/RtmpodWni4/downloaded_packages’
Installation path not writeable, unable to update packages: AlgDesign, asnipe,
  backports, BayesianTools, bayesm, BB, BDgraph, BH, bio3d, blob, bnlearn,
  bridgesampling, broom, calibrate, callr, car, carData, caTools, chron,
  circlize, classInt, cli, clipr, clustree, coin, compositions, cowplot, crul,
  cubature, curl, data.table, DBI, ddalpha, deldir, dendextend, Deriv, deSolve,
  devtools, DHARMa, digest, doMC, doParallel, doSNOW, DT, dtangle, DTRreg, dtw,
  e1071, ellipsis, energy, extRemes, FactoMineR, farver, feather, fields, FME,
  foreach, forecast, foreign, fracdiff, future, gamlss, gamlss.dist, gee,
  geepack, geometry, ggforce, ggplot2, ggraph, ggvis, GillespieSSA, glasso,
  gllvm, glmnet, GlobalOptions, globals, gmm, goftest, h2o, haven, hdf5r,
  hexbin, Hmisc, hms, htmlTable, htmltools, htmlwidgets, httpuv, httr, huge,
  igraph, iterators, jomo, jpeg, kernlab, KernSmooth, knitr, kohonen, ks,
  labdsv, lambda.r, later, lava, lavaan, libcoin, limSolve, liquidSVM, listenv,
  logspline, lpSolve, magick, maptools, markdown, Matrix, matrixStats, mclust,
  MCMCpack, mediation, metap, mgcv, mice, mime, miscTools, mlogit, mlr, modelr,
  mpath, msm, multcomp, multicool, network, nlme, OceanView, openssl, openxlsx,
  optmatch, optparse, ordinal, ParamHelpers, partykit, pbapply, pkgbuild,
  pkgconfig, plot3D, plotly, plotrix, pls, plyr, polspline, pracma, pROC,
  processx, prodlim, promises, pulsar, purrr, pvclust, qgraph, qrnn, quadprog,
  quantreg, R.cache, R.oo, R.rsp, R.utils, R6, randomForestSRC, raster, Rcpp,
  RcppArmadillo, RcppEigen, RcppGSL, Rdpack, recipes, rematch2, reticulate,
  rgl, ritis, RItools, RJSONIO, rlang, rlecuyer, rmarkdown, rms, RNeXML,
  rootSolve, rotl, roxygen2, rrcov, RSNNS, RSQLite, rversions, rvest, RWeka,
  RWekajars, scales, SDMTools, seewave, segmented, selectr, seqinr, shiny,
  slam, sna, solrium, sp, spam, SparseM, spatstat, spatstat.utils, spData,
  strucchange, SuperLearner, survival, svd, sys, taxize, testthat, tidyr,
  tidyverse, timereg, tinytex, tm, TraMineR, TTR, units, uroot, usethis, vctrs,
  vegan, VGAM, vioplot, visNetwork, webshot, whisker, worrms, WriteXLS, xfun,
  XML, xml2, zip, zoo
Skipping install of 'nLTT' from a github remote, the SHA1 (506c9af1) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'beautier' from a github remote, the SHA1 (7387febe) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'tracerer' from a github remote, the SHA1 (714ae526) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'beastier' from a github remote, the SHA1 (aeaa4148) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'mauricer' from a github remote, the SHA1 (e0252fc2) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'babette' from a github remote, the SHA1 (48e5fee3) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'mcbette' from a github remote, the SHA1 (5a705c2b) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'nodeSub' from a github remote, the SHA1 (8dad26e6) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'pirouette' from a github remote, the SHA1 (c4ab5069) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'mbd' from a github remote, the SHA1 (17c2c1fe) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'mbd.SimTrees' from a github remote, the SHA1 (8fd3bd9d) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'becosys' from a github remote, the SHA1 (40a4aa80) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'peregrine' from a github remote, the SHA1 (3ba8e924) has not changed since last install.
  Use `force = TRUE` to force installation
Skipping install of 'razzo' from a github remote, the SHA1 (3112ed14) has not changed since last install.
  Use `force = TRUE` to force installation
Error: HTTP error 403.
  API rate limit exceeded for 129.125.60.88. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

  Rate limit remaining: 0/60
  Rate limit reset at: 2019-12-19 11:10:05 UTC

  To increase your GitHub API rate limit
  - Use `usethis::browse_github_pat()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.
Execution halted

###############################################################################
Peregrine Cluster
Job 9087021 for user 'p230198'
Finished at: Thu Dec 19 11:25:08 CET 2019

Job details:
============

Name                : 1_install_razzo
User                : p230198
Partition           : gelifes
Nodes               : pg-node211
Cores               : 1
State               : FAILED
Submit              : 2019-12-19T11:22:51
Start               : 2019-12-19T11:22:52
End                 : 2019-12-19T11:25:08
Reserved walltime   : 01:00:00
Used walltime       : 00:02:16
Used CPU time       : 00:01:48 (efficiency: 79.61%)
% User (Computation): 82.96%
% System (I/O)      : 17.04%
Mem reserved        : 1G/node
Max Mem used        : 85.96M (pg-node211)
Max Disk Write      : 27.85M (pg-node211)
Max Disk Read       : 330.49M (pg-node211)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################

Guess that's no more Peregrine for me today ...

richelbilderbeek commented 4 years ago

razzo v0.7 has arrived :sunrise_over_mountains:, re-running :rainbow:

richelbilderbeek commented 4 years ago

Works!

razzo_project_20190106.zip