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Hi Benda, |
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|
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[Sending this to gentoo-science mailing list as accidentally replied |
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direct, have also discovered a few other packages that have incorrect |
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versions] |
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|
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Hi Benda, |
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|
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Thanks for taking the time to resolve this, that has worked nicely and Rcpp |
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now emerges. |
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|
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I continued trying to replace all the packages I have installed directly |
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through R with emerges from R_Overlay and opted to emerge the meta-package |
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tidyverse which pulls in a ton of packages as well as more explicit |
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packages that aren't pulled in. In doing so I've encountered three |
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problems.... |
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|
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|
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1. Some ebuilds try to pull in old versions. |
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2. Some ebuilds from R_Overlay require "USE=minimal dev-lang/R" whilst |
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others require "USE=-minimal dev-lang/R" which makes it difficult to emerge |
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things. |
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3. I found one package that is on CRAN but for which there is no ebuild. |
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|
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|
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|
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1. Old Versions |
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============ |
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|
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I found the following old version were pulled in.... |
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|
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| Package | R_Overlay Version | CRAN version | |
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|-----------|-------------------|---------------| |
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| xml2 | 0.1.2 | 1.2.0 | |
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| lubridate | 1.7.0 | 1.7.3 | |
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|
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|
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|
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2. dev-lang/R [-]minimal conflicts |
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========================== |
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|
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Tried emerging a bundle of packages and get conflicts relating to the |
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USE=minimal, also resulted in some slot conflicts that I couldn't see. Its |
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mostly the 'virtual/[pkg]' that require -minimal.... |
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|
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emerge -av ggridges ggraph ggrepel ggnetwork ggmosaic gglasso ggimage |
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ggforce gge ggalt ggROC ggHorizon ggExtra ggbeeswarm lme4 glmnet rpart |
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caret survival Hmisc rms epitools pwr TrialSize longpower simglm |
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clusterPower samplesize PowerTOST blockrand bookdown |
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... |
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|
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!!! Multiple package instances within a single package slot have been pulled |
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!!! into the dependency graph, resulting in a slot conflict: |
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|
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dev-lang/R:0 |
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|
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(dev-lang/R-3.4.4:0/0::slack, installed) pulled in by |
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dev-lang/R[-minimal] required by (virtual/cluster-0:0/0::R_Overlay, |
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ebuild scheduled for merge) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/KernSmooth-0:0/0::R_Overlay, |
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installed) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/MASS-0:0/0::R_Overlay, |
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installed) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/Matrix-0:0/0::R_Overlay, |
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installed) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/codetools-0:0/0::R_Overlay, |
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ebuild scheduled for merge) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/class-0:0/0::R_Overlay, |
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ebuild scheduled for merge) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/foreign-0:0/0::R_Overlay, |
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installed) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/lattice-0:0/0::R_Overlay, |
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installed) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/nlme-0:0/0::R_Overlay, |
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installed) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/survival-0:0/0::R_Overlay, |
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ebuild scheduled for merge) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/rpart-0:0/0::R_Overlay, |
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ebuild scheduled for merge) |
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^^^^^^^^ |
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|
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dev-lang/R[-minimal] required by (virtual/nnet-0:0/0::R_Overlay, ebuild |
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scheduled for merge) |
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^^^^^^^^ |
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|
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|
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(dev-lang/R-3.4.4:0/0::slack, ebuild scheduled for merge) pulled in by |
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dev-lang/R[minimal] required by (sci-CRAN/Matrix-1.2.12:0/0::R_Overlay, |
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ebuild scheduled for merge) |
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^^^^^^^ |
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|
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dev-lang/R[minimal] required by |
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(sci-CRAN/nlme-3.1.131.1:0/0::R_Overlay, ebuild scheduled for merge) |
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^^^^^^^ |
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|
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dev-lang/R[minimal] required by (sci-CRAN/rpart-4.1.13:0/0::R_Overlay, |
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ebuild scheduled for merge) |
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^^^^^^^ |
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|
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dev-lang/R[minimal] required by |
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(sci-CRAN/survival-2.41.3:0/0::R_Overlay, ebuild scheduled for merge) |
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^^^^^^^ |
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|
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dev-lang/R[minimal] required by |
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(sci-CRAN/lattice-0.20.35:0/0::R_Overlay, ebuild scheduled for merge) |
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^^^^^^^ |
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|
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|
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|
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|
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The following USE changes are necessary to proceed: |
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(see "package.use" in the portage(5) man page for more details) |
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# required by sci-CRAN/survival-2.41.3::R_Overlay |
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# required by sci-CRAN/multcomp-1.4.8::R_Overlay |
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# required by sci-CRAN/rms-5.1.2::R_Overlay |
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# required by rms (argument) |
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>=dev-lang/R-3.4.4 minimal |
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|
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|
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Strangely virtual/rpart is listed as requiring USE=-minimal but the rpart |
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package itself requires USE=minimal. |
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|
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|
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3. Missing ebuild for one package |
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========================== |
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|
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I was going to try emergeing the blogdown package ( |
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https://cran.r-project.org/web/packages/blogdown/) but there is no ebuild |
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for it in R_Overlay... |
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|
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# emerge -av blogdown |
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|
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emerge: there are no ebuilds to satisfy "blogdown". |
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|
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emerge: searching for similar names... |
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emerge: Maybe you meant any of these: sci-CRAN/bookdown, sci-BIOC/ballgown, |
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app-admin/logmon? |
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|
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|
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|
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|
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One minor caeveat is that I'm using a locally bumped version of R as the |
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bugreport I've filed for bumping in portage (https://bugs.gentoo.org/632364) |
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hasn't been addressed yet. I'm currently using =dev-lang/R-3.4.4 |
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|
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I'm unsure how the ebuilds in R_Overlay are generated, is it automatically |
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based on available builds? |
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|
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Thanks for yours and others work on this, having R packages managed by |
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portage is a real boon, as it removes the need to update.packages(ask = |
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FALSE) so regularly. |
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|
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If there is something I can do to help please let me know. |
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|
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Neil |
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|
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|
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-- |
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*Natural selection is a mechanism for generating an exceedingly high **degree |
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of improbability.* - R.A. Fisher |
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|
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*Ignorance more frequently begets confidence than does knowledge* - by |
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Charles Darwin |
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|
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PGP Public : https://pgp.mit.edu/pks/lookup?op=get&search=0x0E7ECE9C10D7B4A0 |
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|
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Website - http://kimura.no-ip.info/ |
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Photos - http://www.flickr.com/photos/slackline/ |