Paul J. McMurdie
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/phyloseq |
| Branch: RELEASE_3_6 |
| Last Commit: c695323 |
| Last Changed Date: 2017-11-04 20:23:08 -0400 (Sat, 04 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:21:32 -0400 (Thu, 12 Apr 2018).
| Package 1035/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phyloseq 1.22.3 Paul J. McMurdie
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: phyloseq |
| Version: 1.22.3 |
| Command: rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/phyloseq_1.22.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=phyloseq.buildbin-libdir --merge-multiarch phyloseq_1.22.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL phyloseq_1.22.3.zip && rm phyloseq_1.22.3.tar.gz phyloseq_1.22.3.zip |
| StartedAt: 2018-04-11 18:32:47 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:36:49 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 241.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/phyloseq_1.22.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=phyloseq.buildbin-libdir --merge-multiarch phyloseq_1.22.3.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL phyloseq_1.22.3.zip && rm phyloseq_1.22.3.tar.gz phyloseq_1.22.3.zip
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install for i386
* installing *source* package 'phyloseq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'phyloseq'
finding HTML links ... done
DPCoA html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/DPCoA.Rd:46: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/DPCoA.Rd:13: missing file link 'phylo'
JSD html
UniFrac-methods html
finding level-2 HTML links ... done
access html
assign-otu_table html
assign-phy_tree html
assign-sample_data html
assign-sample_names html
assign-tax_table html
assign-taxa_are_rows html
assign-taxa_names html
build_tax_table html
capscale-phyloseq-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/capscale-phyloseq-methods.Rd:36: missing file link 'rda'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/capscale-phyloseq-methods.Rd:40: missing file link 'rda'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/capscale-phyloseq-methods.Rd:65: missing file link 'rda'
cca-rda-phyloseq-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/cca-rda-phyloseq-methods.Rd:47: missing file link 'rda'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/cca-rda-phyloseq-methods.Rd:48: missing file link 'capscale.phyloseq'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/cca-rda-phyloseq-methods.Rd:42: missing file link 'rda'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/cca-rda-phyloseq-methods.Rd:57: missing file link 'rda'
chunkReOrder html
data-GlobalPatterns html
data-enterotype html
data-esophagus html
data-soilrep html
decorana html
dist-class html
distance html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/distance.Rd:45: missing file link 'UniFrac'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/distance.Rd:46: missing file link 'UniFrac'
distanceMethodList html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/distanceMethodList.Rd:14: missing file link 'UniFrac'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/distanceMethodList.Rd:15: missing file link 'UniFrac'
envHash2otu_table html
estimate_richness html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/estimate_richness.Rd:58: missing file link 'estimateR'
export_env_file html
export_mothur_dist html
extract-methods html
filter_taxa html
filterfun_sample html
fix_phylo html
gapstat_ord html
genefilter_sample-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/genefilter_sample-methods.Rd:49: missing file link 't'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/genefilter_sample-methods.Rd:66: missing file link 't'
get.component.classes html
get_sample-methods html
get_taxa-methods html
get_taxa_unique html
get_variable html
getslots.phyloseq html
import html
import_RDP_cluster html
import_RDP_otu html
import_biom html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:43: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:51: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:60: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:67: missing file link 'readDNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:74: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:163: missing file link 'biom_data'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:165: missing file link 'sample_metadata'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_biom.Rd:167: missing file link 'observation_metadata'
import_env_file html
import_mothur html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_mothur.Rd:75: missing file link 'phylo'
import_mothur_constaxonomy html
import_mothur_dist html
import_mothur_groups html
import_mothur_otu_table html
import_mothur_otulist html
import_mothur_shared html
import_pyrotagger_tab html
import_qiime html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_qiime.Rd:42: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_qiime.Rd:50: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_qiime.Rd:59: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_qiime.Rd:66: missing file link 'readDNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/import_qiime.Rd:73: missing file link 'XStringSet'
import_qiime_otu_tax html
import_qiime_sample_data html
import_uparse html
import_usearch_uc html
index_reorder html
intersect_taxa html
make_network html
merge_phyloseq html
merge_phyloseq_pair-methods html
merge_samples-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/merge_samples-methods.Rd:45: missing file link 'phylo'
merge_taxa-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/merge_taxa-methods.Rd:33: missing file link 'phylo'
metaMDS html
microbio_me_qiime html
mt-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/mt-methods.Rd:50: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/mt-methods.Rd:54: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/mt-methods.Rd:57: missing file link 'p.adjust.methods'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/mt-methods.Rd:63: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/mt-methods.Rd:67: missing file link 'mt.minP'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/mt-methods.Rd:89: missing file link 'mt.minP'
nodeplotblank html
nodeplotboot html
nodeplotdefault html
nsamples-methods html
ntaxa-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/ntaxa-methods.Rd:31: missing file link 'phylo'
ordinate html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/ordinate.Rd:35: missing file link 'rda'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/ordinate.Rd:38: missing file link 'capscale.phyloseq'
otu_table-class html
otu_table-methods html
parseTaxonomy-functions html
pcoa html
phy_tree-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phy_tree-methods.Rd:8: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phy_tree-methods.Rd:33: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phy_tree-methods.Rd:25: missing file link 'phylo'
phylo-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phylo-class.Rd:7: missing file link 'ape'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phylo-class.Rd:12: missing file link 'phylo'
phylo html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phylo.Rd:12: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phylo.Rd:33: missing file link 'phylo'
phyloseq-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phyloseq-class.Rd:12: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phyloseq-class.Rd:40: missing file link 'phylo'
phyloseq-deprecated html
phyloseq-package html
phyloseq html
phyloseq_to_deseq2 html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phyloseq_to_deseq2.Rd:26: missing file link 'DESeqDataSetFromMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/phyloseq_to_deseq2.Rd:60: missing file link 'DESeqDataSetFromMatrix'
phyloseq_to_metagenomeSeq html
plot_bar html
plot_clusgap html
plot_heatmap html
plot_net html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_net.Rd:86: missing file link 'igraph'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_net.Rd:41: missing file link 'layout.auto'
plot_network html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_network.Rd:69: missing file link 'layout.fruchterman.reingold'
plot_ordination html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_ordination.Rd:58: missing file link 'scale_color_manual'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_ordination.Rd:67: missing file link 'scale_shape_manual'
plot_phyloseq-methods html
plot_richness html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_richness.Rd:36: missing file link 'scale_color_manual'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_richness.Rd:48: missing file link 'scale_shape_manual'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/plot_richness.Rd:127: missing file link 'estimateR'
plot_scree html
plot_tree html
prune_samples-methods html
prune_taxa-methods html
psmelt html
rank_names html
rarefy_even_depth html
read_tree html
read_tree_greengenes html
reconcile_categories html
refseq-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/refseq-methods.Rd:8: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/refseq-methods.Rd:33: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/refseq-methods.Rd:25: missing file link 'phylo'
rm_outlierf html
sample_data-class html
sample_data-methods html
sample_names-methods html
sample_sums html
sample_variables html
show-methods html
show_mothur_cutoffs html
splat.phyloseq.objects html
subset_ord_plot html
subset_samples-methods html
subset_taxa-methods html
tax_glom html
tax_table-methods html
taxa_are_rows-methods html
taxa_names-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/taxa_names-methods.Rd:34: missing file link 'phylo'
taxa_sums html
taxonomyTable-class html
threshrank html
threshrankfun html
tip_glom html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/tip_glom.Rd:12: missing file link 'phylo'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpCMEVQc/R.INSTALL127074a5501/phyloseq/man/tip_glom.Rd:68: missing file link 'phylo'
topf html
topk html
topp html
transformcounts html
transpose-methods html
tree_layout html
** building package indices
** installing vignettes
'phyloseq-FAQ.Rmd' using 'UTF-8'
'phyloseq-analysis.Rmd'
'phyloseq-basics.Rmd'
'phyloseq-mixture-models.Rmd'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.22.3.zip
* DONE (phyloseq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'phyloseq' successfully unpacked and MD5 sums checked
In R CMD INSTALL