Paul J. McMurdie
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/phyloseq |
| Branch: RELEASE_3_7 |
| Last Commit: 829992f |
| Last Changed Date: 2018-07-15 15:50:17 -0400 (Sun, 15 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:36:02 -0400 (Wed, 17 Oct 2018).
| Package 1092/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phyloseq 1.24.2 Paul J. McMurdie
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: phyloseq |
| Version: 1.24.2 |
| Command: rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phyloseq.buildbin-libdir phyloseq_1.24.2.tar.gz |
| StartedAt: 2018-10-17 06:47:32 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 06:48:19 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 47.5 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: phyloseq_1.24.2.zip |
| PackageFileSize: 4.362 MiB |
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### Running command:
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### rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phyloseq.buildbin-libdir phyloseq_1.24.2.tar.gz
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install for i386
* installing *source* package 'phyloseq' ...
** R
** data
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/DPCoA.Rd:46: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/DPCoA.Rd:13: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/capscale-phyloseq-methods.Rd:36: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/capscale-phyloseq-methods.Rd:40: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/capscale-phyloseq-methods.Rd:65: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
cca-rda-phyloseq-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/cca-rda-phyloseq-methods.Rd:47: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/cca-rda-phyloseq-methods.Rd:48: file link 'capscale.phyloseq' in package 'phyloseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/cca-rda-phyloseq-methods.Rd:42: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/cca-rda-phyloseq-methods.Rd:57: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/distance.Rd:45: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/distance.Rd:46: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
distanceMethodList html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/distanceMethodList.Rd:14: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/distanceMethodList.Rd:15: file link 'UniFrac' in package 'phyloseq' does not exist and so has been treated as a topic
envHash2otu_table html
estimate_richness html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/estimate_richness.Rd:58: file link 'estimateR' in package 'vegan' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/genefilter_sample-methods.Rd:49: file link 't' in package 'phyloseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/genefilter_sample-methods.Rd:66: file link 't' in package 'phyloseq' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:43: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:51: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:60: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:67: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:74: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:163: file link 'biom_data' in package 'biomformat' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:165: file link 'sample_metadata' in package 'biomformat' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_biom.Rd:167: file link 'observation_metadata' in package 'biomformat' does not exist and so has been treated as a topic
import_env_file html
import_mothur html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_mothur.Rd:75: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_qiime.Rd:42: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_qiime.Rd:50: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_qiime.Rd:59: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_qiime.Rd:66: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/import_qiime.Rd:73: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/merge_samples-methods.Rd:45: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
merge_taxa-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/merge_taxa-methods.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
metaMDS html
microbio_me_qiime html
mt-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/mt-methods.Rd:50: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/mt-methods.Rd:54: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/mt-methods.Rd:57: file link 'p.adjust.methods' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/mt-methods.Rd:63: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/mt-methods.Rd:67: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/mt-methods.Rd:89: file link 'mt.minP' in package 'multtest' does not exist and so has been treated as a topic
nodeplotblank html
nodeplotboot html
nodeplotdefault html
nsamples-methods html
ntaxa-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/ntaxa-methods.Rd:31: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
ordinate html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/ordinate.Rd:35: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/ordinate.Rd:38: file link 'capscale.phyloseq' in package 'phyloseq' does not exist and so has been treated as a topic
otu_table-class html
otu_table-methods html
parseTaxonomy-functions html
pcoa html
phy_tree-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phy_tree-methods.Rd:8: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phy_tree-methods.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phy_tree-methods.Rd:25: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
phylo-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phylo-class.Rd:7: file link 'ape' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phylo-class.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
phylo html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phylo.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phylo.Rd:33: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
phyloseq-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phyloseq-class.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phyloseq-class.Rd:40: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
phyloseq-deprecated html
phyloseq-package html
phyloseq html
phyloseq_to_deseq2 html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phyloseq_to_deseq2.Rd:26: file link 'DESeqDataSetFromMatrix' in package 'DESeq2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/phyloseq_to_deseq2.Rd:60: file link 'DESeqDataSetFromMatrix' in package 'DESeq2' does not exist and so has been treated as a topic
phyloseq_to_metagenomeSeq html
plot_bar html
plot_clusgap html
plot_heatmap html
plot_net html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_net.Rd:86: file link 'igraph' in package 'igraph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_net.Rd:41: file link 'layout.auto' in package 'igraph' does not exist and so has been treated as a topic
plot_network html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_network.Rd:69: file link 'layout.fruchterman.reingold' in package 'igraph' does not exist and so has been treated as a topic
plot_ordination html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_ordination.Rd:58: file link 'scale_color_manual' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_ordination.Rd:67: file link 'scale_shape_manual' in package 'ggplot2' does not exist and so has been treated as a topic
plot_phyloseq-methods html
plot_richness html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_richness.Rd:36: file link 'scale_color_manual' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_richness.Rd:48: file link 'scale_shape_manual' in package 'ggplot2' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/plot_richness.Rd:127: file link 'estimateR' in package 'vegan' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/refseq-methods.Rd:8: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/refseq-methods.Rd:33: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/refseq-methods.Rd:25: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
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-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/taxa_names-methods.Rd:34: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
taxa_sums html
taxonomyTable-class html
threshrank html
threshrankfun html
tip_glom html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/tip_glom.Rd:12: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpe6x5xC/R.INSTALLe142e85366e/phyloseq/man/tip_glom.Rd:68: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
topf html
topk html
topp html
transformcounts html
transpose-methods html
tree_layout html
** building package indices
** installing vignettes
** 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_1.24.2.zip
* DONE (phyloseq)
In R CMD INSTALL
In R CMD INSTALL