Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:20 -0400 (Sat, 23 Oct 2021).

CHECK results for BloodGen3Module on riesling1

To the developers/maintainers of the BloodGen3Module package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BloodGen3Module.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 204/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BloodGen3Module 1.1.1  (landing page)
Darawan Rinchai
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/BloodGen3Module
git_branch: master
git_last_commit: 627196f
git_last_commit_date: 2021-09-16 04:35:21 -0400 (Thu, 16 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BloodGen3Module
Version: 1.1.1
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BloodGen3Module.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BloodGen3Module_1.1.1.tar.gz
StartedAt: 2021-10-23 05:12:16 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 05:19:15 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 418.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BloodGen3Module.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BloodGen3Module.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BloodGen3Module_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BloodGen3Module.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BloodGen3Module/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BloodGen3Module' version '1.1.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BloodGen3Module' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
  Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
  Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
  Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
See 'D:/biocbuild/bbs-3.14-bioc/meat/BloodGen3Module.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
Groupcomparison      13.03   1.27   15.05
gridplot             10.36   0.16   10.92
fingerprintplot       6.27   0.22    6.92
Groupcomparisonlimma  5.90   0.15    6.58
Individualcomparison  5.39   0.19    5.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
Groupcomparison      13.72   1.16   15.67
gridplot             11.18   0.18   11.82
fingerprintplot       6.51   0.19    7.17
Groupcomparisonlimma  6.41   0.20    7.11
Individualcomparison  5.44   0.17    6.15
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-fold_change.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-fold_change.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.14-bioc/meat/BloodGen3Module.Rcheck/00check.log'
for details.



Installation output

BloodGen3Module.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BloodGen3Module_1.1.1.tar.gz && rm -rf BloodGen3Module.buildbin-libdir && mkdir BloodGen3Module.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BloodGen3Module.buildbin-libdir BloodGen3Module_1.1.1.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BloodGen3Module_1.1.1.zip && rm BloodGen3Module_1.1.1.tar.gz BloodGen3Module_1.1.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  172k  100  172k    0     0   901k      0 --:--:-- --:--:-- --:--:--  906k

install for i386

* installing *source* package 'BloodGen3Module' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
** help
*** installing help indices
  converting help for package 'BloodGen3Module'
    finding HTML links ... done
    Gen3_ann                                html  
    Groupcomparison                         html  
    Groupcomparisonlimma                    html  
    Individualcomparison                    html  
    Module_listGen3                         html  
    color                                   html  
    fingerprintplot                         html  
    fold_change                             html  
    gridplot                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BloodGen3Module' ...
** testing if installed package can be loaded
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
* MD5 sums
packaged installation of 'BloodGen3Module' as BloodGen3Module_1.1.1.zip
* DONE (BloodGen3Module)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BloodGen3Module' successfully unpacked and MD5 sums checked

Tests output

BloodGen3Module.Rcheck/tests_i386/test-fold_change.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("gtools")
> library("testthat")
> library("BloodGen3Module")
Warning messages:
1: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module' 
2: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module' 
3: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module' 
4: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module' 
> 
> fold_change = function(df_raw = df_raw,
+                        sample_info = sample_info,
+                        Group_column = Group_column,
+                        Test_group=Test_group,
+                        Ref_group=Ref_group){
+ 
+   FC.group = data.frame(matrix(ncol = 1, nrow = nrow(df_raw)))
+   colnames(FC.group) = Test_group
+   rownames(FC.group) = rownames(df_raw)
+ 
+   for (k in 1:nrow(df_raw)) {
+     signature = rownames(df_raw)[k]
+     test.table <- sample_info
+     test.table$scores <- df_raw[k,]
+     T2 <- test.table[test.table[, Group_column]==Test_group,]       # "Group_test"; the selected column could be changed to your interested group comparison
+     T1 <- test.table[test.table[, Group_column]==Ref_group,]        # "Group_test"; the selected column could be changed to your interested group comparison
+     FC.group[signature,] <- foldchange(mean(T2$scores),mean(T1$scores))
+   }
+   FCgroup <- data.frame(FC.group)
+ }
> 
> 
> library(ExperimentHub)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

The following object is masked from 'package:ExperimentHub':

    cache

The following object is masked from 'package:AnnotationHub':

    cache

> dat = ExperimentHub()
snapshotDate(): 2021-10-18
> res = query(dat , "GSE13015")
> GSE13015 = res[["EH5429"]]
see ?GSE13015 and browseVignettes('GSE13015') for documentation
loading from cache
> data_matrix = assay(GSE13015)
> sample_ann = data.frame(colData(GSE13015))
> 
> 
> test_that("test fold_change", {
+   a  = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+                                             sample_info = sample_ann,
+                                             Group_column = "Group_test",
+                                             Test_group="Sepsis",
+                                             Ref_group="Control")
+   b  = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+                                             sample_info = sample_ann,
+                                             Group_column = "Group_test",
+                                             Test_group="Sepsis",
+                                             Ref_group="Control")
+ 
+   expect_that(a, equals(b))
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  11.01    1.35   13.14 

BloodGen3Module.Rcheck/tests_x64/test-fold_change.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("gtools")
> library("testthat")
> library("BloodGen3Module")
Warning messages:
1: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module' 
2: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module' 
3: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module' 
4: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module' 
> 
> fold_change = function(df_raw = df_raw,
+                        sample_info = sample_info,
+                        Group_column = Group_column,
+                        Test_group=Test_group,
+                        Ref_group=Ref_group){
+ 
+   FC.group = data.frame(matrix(ncol = 1, nrow = nrow(df_raw)))
+   colnames(FC.group) = Test_group
+   rownames(FC.group) = rownames(df_raw)
+ 
+   for (k in 1:nrow(df_raw)) {
+     signature = rownames(df_raw)[k]
+     test.table <- sample_info
+     test.table$scores <- df_raw[k,]
+     T2 <- test.table[test.table[, Group_column]==Test_group,]       # "Group_test"; the selected column could be changed to your interested group comparison
+     T1 <- test.table[test.table[, Group_column]==Ref_group,]        # "Group_test"; the selected column could be changed to your interested group comparison
+     FC.group[signature,] <- foldchange(mean(T2$scores),mean(T1$scores))
+   }
+   FCgroup <- data.frame(FC.group)
+ }
> 
> 
> library(ExperimentHub)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

The following object is masked from 'package:ExperimentHub':

    cache

The following object is masked from 'package:AnnotationHub':

    cache

> dat = ExperimentHub()
snapshotDate(): 2021-10-18
> res = query(dat , "GSE13015")
> GSE13015 = res[["EH5429"]]
see ?GSE13015 and browseVignettes('GSE13015') for documentation
loading from cache
> data_matrix = assay(GSE13015)
> sample_ann = data.frame(colData(GSE13015))
> 
> 
> test_that("test fold_change", {
+   a  = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+                                             sample_info = sample_ann,
+                                             Group_column = "Group_test",
+                                             Test_group="Sepsis",
+                                             Ref_group="Control")
+   b  = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+                                             sample_info = sample_ann,
+                                             Group_column = "Group_test",
+                                             Test_group="Sepsis",
+                                             Ref_group="Control")
+ 
+   expect_that(a, equals(b))
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  10.68    1.48   12.95 

Example timings

BloodGen3Module.Rcheck/examples_i386/BloodGen3Module-Ex.timings

nameusersystemelapsed
Groupcomparison13.03 1.2715.05
Groupcomparisonlimma5.900.156.58
Individualcomparison5.390.195.97
fingerprintplot6.270.226.92
fold_change2.350.122.98
gridplot10.36 0.1610.92

BloodGen3Module.Rcheck/examples_x64/BloodGen3Module-Ex.timings

nameusersystemelapsed
Groupcomparison13.72 1.1615.67
Groupcomparisonlimma6.410.207.11
Individualcomparison5.440.176.15
fingerprintplot6.510.197.17
fold_change2.390.123.01
gridplot11.18 0.1811.82